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- In the new opening of the Unrated Edition, Karl has the top two buttons on his shirt undone as he runs through Razorback Point, but when he falls to the ground as the Predator approaches him inside the hut, his shirt is completely buttoned up.
- When we first meet Lex climbing the icefall, she is some fifty meters or so from the top, yet when Stafford phones her, she reaches the summit within mere moments. The first wide shot of the icefall also makes it clear there is nothing at the top of the plateau, but when Lex gets there Stafford has suddenly arrived by helicopter, even though we never heard a helicopter land. What's more, the chopper's rotors are totally stationary, when in reality it takes some time for rotors to come to a complete halt after a helicopter is powered down, and certainly longer than the intervening time shown in the film.
- When the icebreaker Piper Maru is seen cutting through the ice in closeup, it clearly has a rounded prow, as all icebreaking vessels do. However, the ship is later seen with an angled prow, which is not only inconsistent with what was shown in closeup earlier, it is totally incorrect for an icebreaker ship.
- When the team first reaches the whaling camp, Lex says the pyramid is "directly beneath" the settlement. However, Quinn later states the access shaft bored to it by the Predators is at a perfect 30 degree angle. If the shaft starts in Razorback Point and descends some 2,000 feet vertical distance at a constant angle of 30°, the pyramid cannot possibly be directly below the settlement. In fact, a schematic that Weyland looks at before the team head down confirms that the pyramid is a considerable distance away from Razorback Point.
- When the first group descends the tunnel, it is clearly shown that there are only six cables coming from the winch used to lower them down. However, subsequent shots show eight people in the group, each attached to a separate cable, plus a crate of supplies that would likely require an additional cable of its own.
- Lex uses her ice axe to stop Weyland from sliding down the ice tunnel, stabbing it into the ice ahead of him so that his coat catches on it as he slides past. However, in the subsequent shot, it is stabbed through the hood of his jacket.
- Lex is wearing a silver jacket over her red cold weather clothing at the start of the expedition, but when Stafford splits the group up in the sacrificial chamber she is visible in the background no longer wearing it. From this point on her jacket is never seen again, and no explanation is given as to why she removed it or where it went.
- When Rousseau first notices the Eggs arriving in the sacrificial chamber, she is standing just in front of the circular grate in the center of the floor. She is then attacked by the Facehugger, which knocks her backwards some distance, away from the grate, but when the camera angle changes to the view from below, she lands directly on top of the grate.
- The transparent magazine in Stafford's G36C is visibly almost empty when he first draws and readies the weapon, despite the fact it has yet to be fired.
- According to the earlier films in the franchise, Chestburster implantation is supposed to take around 24 hours once a Facehugger attaches to its victim. Yet Rousseau, Miller and Sebastian are all impregnated in a matter of minutes. Scar is also impregnated within 10 minutes; he is up and moving around again before the pyramid next realigns itself. The actual gestation period before the Chestburster emerges also varies wildly in the film — Rousseau dies almost immediately after she regains consciousness, yet the Chestburster inside Scar does not emerge until after his clan have taken his body and left Earth, some time after he was impregnated (the latter being more in line with the previous films in the series).
- As Connors is sealed in the narrow shaft by the shifting pyramid, we see Verheiden standing over him, head down and grimacing. Yet in the next closeup of Verheiden, he has his head up and a totally different shocked expression on his face.
- When Connors falls down the slope inside the shaft, his G36C lands in some slime on what is obviously a flat, level surface (as can be seen from the way it bounces). Yet when he recovers the weapon, it is lying on the steep incline he just fell down. In the Unrated Edition, this sequence is re-edited, leading to an additional goof — in the extended cut, Connor's weapon does not land in slime, yet it is still covered in the substance when he picks it up.
- Bass is killed when he is impaled by Scar's Combistick, but when Stafford later checks over Bass' corpse in the Unrated Edition, there is no hole in his clothing; there is a small amount of blood on his chest where the spear hit him, but no hole torn in the fabric of his coat.
- When Grid impales Chopper, its tail is suddenly vastly longer than at any other point in the film, seemingly more than twenty feet in length. Also, the tail is covered in glowing Predator blood, but when Grid flings Chopper's corpse away, the blood is gone.
- Grid kills Celtic by Headbiting him through the forehead of his mask and it clearly makes a hole. However, in the next shot of Celtic's head falling back, the mask has no puncture hole at all.
- When Scar kills a Xenomorph by slicing off the front of its head, no blood spills from the wound. At every other point in this film (and the rest of the series), Xenomorphs are seen to bleed profusely, even violently, when wounded.
- During the flashback to hunts in ancient times, a victorious Predator lofts a Xenomorph head above him, impaled on its spear. If this were the case, the Predator would surely be burned by the acid blood that would drip from the freshly decapitated head.
- When Miller draws Verheiden's Desert Eagle while they are both cocooned in the Hive, the pistol's safety catch is on (the lever is visibly in the down position, not to mention the fact Miller repeatedly pulls on the trigger to get the weapon out of its holster without it ever going off). Despite this, Miller is somehow able to immediately shoot the Facehugger that is about to attack him.
- When Scar strips the Xenomorph corpse in the Unrated Edition, he pulls a mucus membrane away from the creature's brain with his bare hand, yet he doesn't get burnt by the creature's potent acidic blood.
- When Lex euthanises Sebastian, the Desert Eagle she uses cycles properly in the shot of her firing, yet in the next shot from the side, the slide is suddenly locked back.
- The Chestburster that erupts from Sebastian has no blood on it whatsoever when Scar catches it, despite the fact it has just burst out of a man's chest.
- The spear that Scar makes for Lex is a continuity nightmare in the final act of the film — when the pair flee the Hive, neither of them is holding it. Lex then has it strapped to her back as they run from the pyramid, and when they reach the ice tunnel she places it on the sled. It subsequently disappears as they race up the tunnel, but when the ice starts to collapse outside, Scar is holding it. It then vanishes again as Lex and Scar flee the collapsing ice, only to reappear in Scar's hand as they fall to the floor at the end of the sequence, at which point he drops it. Finally, when Scar gives Lex her initiation mark, she has the spear in her hand without ever having picked it up.
- During the brief fight at the base of the shaft through the ice, Scar is impaled through the shoulder by a Xenomorph's tail. The resulting wound appears and disappears for the rest of the film.
- The number of adult Xenomorphs that appear throughout the film is greater than the number of hosts impregnated — six people are impregnated in the sacrificial chamber and three more Xenomorphs come from Connors, Miller and Verheiden, giving nine in total (while Sebastian is also impregnated, his Chestburster is killed as soon as it emerges); over the course of the movie, Scar kills one Drone with a Shuriken and three more with his Plasmacaster, while Lex kills two, one with Scar's Combistick and one with the bolt gun. This should leave only three adult Xenomorphs remaining, yet just before Lex and Scar flee to the surface on the sled, five adult Xenomorphs are seen.
- When Scar burns the initiation mark into Lex's cheek, she flinches as the acid touches her skin. This clearly causes the first line Scar burns to be jagged, but in every subsequent shot it is perfectly straight.
- The initiation mark appears and disappears between shots as Lex is running around the whaling camp at the end of the film. Her Xenomorph shield also switches between her left and right hands.
- The Queen impales Scar through the chest with her tail, yet the Chestburster inside him somehow survives unharmed.
- Lex is startled by the Ancient Predator decloaking directly beside her. Yet when the camera cuts to the next wide shot, the Predator Mother Ship is nearby, its open doors spilling almost blinding light in their direction. There is no way Lex could have failed to notice such a bright light source aimed directly at her, even from the side.
- After the team inside the pyramid has split to investigate the lower level, Lex checks her compass and says, "This should be directly below the sacrificial chamber." That much should be obvious from the glow stick lying on the floor in front of her, which Stafford dropped down the vertical shaft in the sacrificial chamber floor earlier.
- After Sebastian is taken by Scar, Lex spends the rest of the film walking around without a torch or any other form of illumination. The inside of the pyramid would be pitch black — especially if it is located 2,000 feet under the ice — yet she somehow manages to see her surroundings with no trouble.
- Razorback Point is an incredibly remote Norwegian whaling station dating from the 1900s, yet the sign announcing its name is written in English.
- Satellite images in the film show Bouvet Island as being far further south and west than it is in real life. The geographical location shown in the film actually approximates to Peter I Island, which is almost 3,000 miles from Bouvet.
- The film states that Lex is climbing the "Lho La Ice Fall". However, Lho La is actually a col (the lowest point on a ridge or the saddle between two peaks, typically affording a pass from one side of a mountain range to another) on the border between Nepal and Tibet north of the Western Cwm, near Mount Everest.
- The Piper Maru is said to be pushing through the Ross Ice Shelf when Weyland 14 delivers Lex for the meeting with Weyland — not only is the Ross Ice Shelf hundreds of meters thick and totally impenetrable to any kind of surface vessel, Bouvet Island (even in the erroneous location shown in the film) is nowhere near it. Furthermore, as the shelf fills a large natural bay on the coast of Antarctica, there would be no conceivable need to pass through it to reach the island.
- The film claims or at least strongly implies that Bouvet Island is not under any national control thanks to the Antarctic Treaty. However, because of its remoteness from the continent of Antarctica, Bouvet Island is not actually included in this treaty and in reality Norway has full ownership of the island.
- Several characters, if not the majority of them, carry guns. Under numerous international treaties, it is illegal to bring firearms and other weapons to Antarctica. Most movies set on the continent tend to overlook this. In the novelization, Quinn does actually point this out to Sven, implying the mercenaries are illegally armed, but the film does not address the issue at all.
- When the team arrives in Antarctica, it is night time. However, the story is set in October, which is summertime in the southern hemisphere. South of the Antarctic circle, there would be 24-hour daylight (or, at the very least, a period of twilight instead of outright nightfall) during this time.
- There is a full moon when the team arrives in Antarctica on 10/10/2004, yet there was no full moon there on that date. The closest full moon was actually on 10/28/2004.
- The movie states the whaling station on Bouvet Island was abandoned in October 1904, when in fact it wasn't until November 1904 that the first Antarctic whaling station, Grytviken (Cauldron Bay), was established, and not on Bouvet Island, but in South Georgia. Modern whalers didn't reach Bouvet until the 1928-29 season, and they only operated with factory ships offshore. There has in fact never been a whaling station established on the island.
- When the Weyland Industries team is searching the whaling camp, a penguin startles Miller. The penguin is a Humboldt Penguin (Spheniscus humboldti), which is native to the far warmer region of coastal Peru and Chile and would never be found in Antarctica.
- Sebastian states numerous factual errors regarding the Aztec calendar. He refers to "the Long Count" while describing the Aztec calendar, when the Long Count was actually a feature of the Mayan calendar system; the Aztec calendar, although based on that of the Mayans, didn't use the Long Count. He also erroneously claims that the Aztec calendar was metric (based on 10). In fact, the Aztecs had two calenders and neither was metric; one was vigesimal (based on 20) with twenty days in 13 "months", while the other was a 365-day year count.
- To open the sarcophagus, Sebastian sets the time lock to October 10, 2004 — 10/10/2004. However, this makes no sense, as the ancient Aztec calendar (on which the sarcophagus is supposedly based) would not align with the Julian calendar (upon which our modern calendar is based and which wasn't developed until centuries later by the Romans). Consequently, the Aztecs would not recognize what we call "October" as the 10th month, nor would they recognize the year "2004".
- After Rousseau is attacked by a Facehugger, her screams can be heard by the second group of explorers in the room below the sacrificial chamber, a significant distance away. However, it is highly unlikely she would be able to scream so loudly with a Facehugger smothering her face, especially if the creature had inserted its proboscis down her throat.
- The movie makes it clear that the pyramid reconfigures itself every ten minutes, which Sebastian surmises is because the calendar on the sarcophagus is metric. However, minutes are part of a sexagesimal (based on sixty) system, not metric, and therefore the rearrangement occurring in a matter of minutes is nonsensical. A truly metric time measurement for the rearrangement of the structure would be every one-hundredth of a day (actually 14.4 minutes).
- In the Hive, Miller fires 12 shots from Verheiden's .44 Magnum Desert Eagle, which has a maximum capacity of 9 rounds (8 in the magazine plus 1 more in the chamber). Lex later picks up the pistol and fires another round from it before it is finally empty.
- Lex spends the end of the film running around outside with no protective thermal coat on. Even in summertime, average temperatures in Antarctica are between -10 to -30°C, and she would soon start to experience the debilitating effects of this cold, yet she is never affected.
- The shot of the Queen being dragged into the depths by the iron vat show that the water is apparently hundreds if not thousands of feet deep, which is very unlikely immediately offshore.
- During the wide shot of the Piper Maru with equipment and people moving around alongside it on the ice, the ship itself and the equipment cast shadows, but not the moving people, indicating they were added in later.
- In the Unrated Edition, the scene where Lex, Sebastian and Miller discover the trophy room adjacent to the sacrificial chamber includes a shot of Sebastian's torch beam passing over the skulls mounted on the walls. This shot is actually repeated from just a few moments earlier — the first time it is shown, when the team is first exploring the sacrificial chamber itself, appears in both cuts of the film.
- When the team opens the casket with the three Plasmacasters, the flat ends of the "barrels" can be seen in the shot that passes over the Casters. This is pointed out during Tom Woodruff, Jr. and Alec Gillis' commentary of the film.
- In the shot of Grid headbiting Celtic, a hand can be seen holding the Predator's mask.
- As Scar lays dead at the end of the film, the puncture wound to his torso is clearly painted on top of his armor and not actually a hole.
- The book offers far more insight into the destruction of Razorback Point in 1904 — yet the timeline of events described makes no sense, particularly regarding where the Xenomorphs involved could have come from. The novel makes it clear the incident begins when the whalers recover a Predator within its drop pod on the surface. Almost immediately after the pod is returned to the station, the Predator emerges and begins a killing spree, before Aliens also begin running amok in the settlement. However, none of the whalers have had time to descend to the pyramid below to become hosts for the Xenomorphs at this point, be it voluntarily or as captives of the Predators. In fact, none of the humans are even aware of the pyramid's existence. Furthermore, given that the Predator they recovered was still inside its pod on the surface, the hunters have yet to visit the pyramid either. It is therefore unexplained where the Xenomorphs attacking the camp could have come from.
- An additional mercenary named Peters is with Lex's group when the mercenaries break out their weapons; however, this extra man subsequently disappears.
- Much like the film, the number of adult Xenomorphs that appear later in the story is greater than the number of hosts impregnated, although the discrepancy is exponentially larger in the novel — towards the end of the story, there are said to be "hundreds" of Aliens in the pyramid, despite the fact there were nowhere enough people on the Weyland Industries expedition to be hosts for such a large number of creatures.
- At the end of the book, Lex has Sebastian's Pepsi bottle cap in her pocket, despite the fact it fell into the chasm she jumped across earlier.
- When Lex and Sebastian are discussing how the Predators have visited Earth to hunt before, Lex mentions an "unexplained" nuclear explosion that took place on Bouvet Island in 1979, the implication being the Predators were responsible. This is based on a real event that remains unsolved (the Vela Incident). However, this explosion did not take place on Bouvet Island, but in reality occurred near the Prince Edward Islands, which are over 1,500 miles away. While the cause of the detonation has never been definitively determined, it is thought to have been a nuclear weapons test conducted by South Africa and/or Israel.