- When the Chestburster is removed from Ripley 8, the incision is made below her breasts. Later, the scar is higher up, between her breasts.
- The Queen Chestburster that is removed from Ripley 8 looks like a typical Chestburster seen in the previous films, yet in Alien3 the Queen Chestburster inside Ripley had a unique appearance, with four arms and an already-developing head crest visible on top.
- Ripley 8 has acid blood, apparently potent enough to burn through thick metal and toughened glass. Yet it does no damage to any of the surgical implements used to extract the Chestburster from her at the start of the film.
- When Ripley 8 wakes up during surgery in the extended Special Edition, the surgical incision in her chest is far smaller than the one seen earlier when the Chestburster was actually removed.
- During Dr. Gediman's discussion with Ripley 8 regarding her origins, he says she was cloned using "blood samples from Fiori 16, on ice". However, the planet's name (from Alien3) is actually Fiorina 161, nicknamed "Fury".
- When Call confronts Johner aboard the Betty, she places the wrench she is holding down on a surface. However, it falls off after she places it. Not only is there no sound of it hitting the floor, but it is suddenly back on top of the surface later on without anyone picking it up.
- When General Perez first pushes the money across to Elgyn during their meeting it ends up sitting right at the edge of the table. It subsequently moves closer to the middle of the table without anyone touching it.
- When Ripley 8 knocks Christie to the floor, we do not see or hear the barbell that he was holding fall to the ground.
- Immediately after the basketball fight, when Wren first appears, Vriess and his P.T.V. disappear in the reverse angle.
- In the scene where Gediman moves the observation module past the cells of Cloned Xenomorphs, we can see that the Aliens only just fit inside the cells, and that their bodies fill up the windows in the front of each cage almost entirely. Yet every time we see these cages subsequently, they are big enough for as many as three Xenomorphs to fit inside with plenty of room to spare, and the creatures appear far smaller in the windows.
- When Call stabs Ripley 8 through the hand, the blood on the blade and the wound on Ripley 8's hand come and go between shots.
- When Christie draws his Wrist Guns, his hands are behind his back. In the next shot, they are hanging by his sides.
- The legs of the Xenomorphs differ between the practical suits and the CGI creatures, with the former having plantigrade legs while the latter have digitigrade legs.
- When the Xenomorph reaches up through the grating and Elgyn is shown getting pulled down, there is a big hole burned into the grate in front of him that was not there just a second before. There are also chunks of gore lying around that appear out of nowhere.
- When the survivors are cornered by a Xenomorph after Elgyn is killed, Distephano points out that they cannot shoot the creature because it is in front of the hull. Not only has gunfire been happening for half an hour or so before this (most notably heard off-screen during the initial break out) without anyone rupturing the Auriga's hull, Ripley 8 actually shoots the Xenomorph just moments later without causing any damage to the ship. Moreover, it virtually explodes when it is shot, yet its acid blood, which was previously powerful enough to melt through multiple decks in mere moments when the Xenomorphs first escape, does no damage whatsoever to any of the surrounding surfaces.
- Before the survivors discover the lab holding the failed clones, nine people walk past the camera. However, there are only eight survivors in the group at that point in the film, as they have yet to find Purvis.
- Following the swim through the flooded mess, the survivors' clothes dry almost immediately after exiting the water. Only Call stays wet as one would naturally expect.
- The Newborn's mouth is dripping blood when it bites into Gediman's head, yet when it turns to Ripley 8 and roars in the next shot, the blood is gone.
- A large volume of steam is flowing under the Betty's jammed cargo door as Call attempts to close it, totally obscuring what is outside, but in the next shot of the ship's exterior the air outside is clear; while a small amount of steam can be seen coming from two vents on the ship's hull, these are at the front of the ship, whereas the cargo door is at the rear, and regardless, they are not putting out anything like enough steam to create the effect seen inside the cargo bay.
- The blood spattered on Call's face when she is with the Newborn disappears.
- There is no blood on the Newborn's hand when it caresses Ripley 8's face, even though it crushed Distephano's head just moments earlier.
- In the theatrical cut, the final shots of Ripley 8 and Call looking down at Earth from the Betty clearly show that the vessel is at incredibly high altitude, if not in orbit, yet in the preceding shots it was flying through the cloud layer.
- In the previous Alien movies, the victims of Chestbursters have been completely incapacitated by pain during the "birth", yet when the infant inside Purvis begins to emerge he is able to walk around the room and even give Wren a brutal, prolonged beating.
- The potential danger of gunfire rupturing the Auriga's hull is pointed out several times during the course of the movie. However, if this is such a threat, why are the soldiers stationed on board even issued rifles at all if they cannot safely fire them? Some other form of weaponry that would not endanger the ship would make far more sense, such as the electrical shock devices fitted to the assault rifles some of the men carry. What's more, even today, specialized ammunition types are available for use in just such a situation, where collateral damage from over-penetration poses a risk; for example, doctored rounds with a low-impact charge are issued to air marshals aboard commercial flights so that they can use their weapons without penetrating the aircraft's fuselage. It seems unlikely future weapons would be incapable of incorporating such technology.
- Wren claims there are twelve Xenomorphs remaining when asked how many more of the creatures exist. However, given that at least some of the creatures have evidently been killed during the breakout, he could not possibly know this with any certainty at the time he says it.
- The survivors find the bodies of the kidnapped Xenomorph hosts in the room where they encounter Purvis; it has clearly been at least a day since the Xenomorphs were born, so why are these bodies still lying around, some of them still held in the restraints they were put in for impregnation? Even from a basic sanitary point of view, it makes no sense that these corpses would be left to rot in the fashion they are discovered in the movie, especially aboard a highly efficient scientific research ship. The risk of disease alone makes this scenario totally illogical.
- The Chestburster inside Purvis does not emerge until the very end of the film, despite the fact every other colonist who was impregnated at the same time as him died many hours or even days earlier. Although the film's novelization states Purvis suffers from a low thyroid count, slowing the Chestburster's development, this information is never given in the film, leaving a glaring plot hole.
- Shock and sound waves travel much further and faster underwater, and as a result, everyone should have been killed, seriously injured, or at the very least totally deafened, by the grenade that Johner uses to kill one of the Xenomorphs in the flooded mess hall.
- When Purvis attacks Wren aboard the Betty, the doctor shoots him almost a dozen times in the chest at point-blank range, yet this seemingly has no effect on him whatsoever; in fact, Purvis is still able to brutally beat Wren and throw him around the room, despite his numerous gunshot wounds. While it could be argued Purvis' body would be pumping with adrenaline as a result of the imminent Chestburster birth he is experiencing, so many bullet wounds to his chest at such close range would undoubtedly incapacitate a human being, regardless of the amount of adrenaline coursing through their veins.
- Normal air pressure would be nowhere near sufficient to expel the Newborn through a hole as small as the one in the Betty's window, even in space. Moreover, the time it takes for the Newborn to be sucked out of the Betty's window would be more than enough to decompress the entire ship and kill everyone on board. Even if the crew somehow survived, re-entering the Earth's atmosphere with the breach in the hull would incinerate Ripley and Call in the hold and likely destroy the ship.
- When Hillard throws the basket ball at Ripley 8, the white tape stuck to Sigourney Weaver's palm that allows her to catch the ball with one hand is visible.
- The barbell Christie hits Ripley 8 with clearly bends, revealing that it is made of rubber.
- When Johner destroys the Alien underwater, the grenade he fires visibly passes through the front of the creature's head without making any impact before exploding moments later.
- In the first shot of Earth from space, the image has been flipped as Africa is facing in the wrong direction.
- When Gediman begins ranting in the Queen's chamber, the movement of his lips clearly does not match what he is saying. In fact, judging by the movement of his mouth, he is literally saying, "Blah, blah, blah..."
- Gediman mentions that LV-426 is uninhabitable due to radiation caused by the explosion of the Atmosphere Processor at the end of Aliens. However, this contradicts the novelization of that film, which states the detonation of an Atmosphere Processor is clean and does not produce fallout.