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- When Vickers is doing push-ups immediately after waking, she has a small, tight top wrapped around her chest, but this then disappears once she has put on her bath robe.
- When Millburn introduces himself to Fifield, his accent suggests he is from the southern United States. For the rest of the film, this accent is gone.
- The small tattoo above Fifield's left eye occasionally disappears throughout the film.
- When he releases his PUPS inside the Engineer temple, Fifield suddenly has wipe marks inside his helmet that were not there before, and which disappear in subsequent shots. Not only is this inconsistent, there is no way Fifield could wipe the condensation from inside his helmet without removing it, which he does not do until much later.
- As the group explore the tunnels of the temple after removing their helmets, Ford states, "It's minus twelve in here." If it was really so cold, we would be able to see very noticeable vapor clouds when the team members breathe, but we do not. Such a low temperature would also affect the team members physically with their heads uncovered as they are, yet it does not.
- In the Ampule room, Shaw sternly warns David not to touch anything, despite the fact he has been touching things and even activating control consoles inside the temple ever since they arrived without anyone uttering a word of complaint.
- At the end of the first day's exploring, when the crew race back to the Prometheus ahead of the storm, they drive the RT Series Group Transport straight into the hangar bay aboard the ship. However, when they head out at the start of the second day, the transport has completely turned around and is facing back towards the doorway, despite there being insufficient room to turn the large vehicle around in the hangar.
- While Shaw and Ford are examining the decapitated Engineer head, we see Holloway jump up onto a medical table in the background. In the very next shot, he is suddenly taking a swig from a bottle of champagne that he was not holding just a moment before.
- When Janek calls Millburn and Fifield to inform them of the sporadic life readings being picked up by one of the PUPS, he asks them where they are inside the temple, despite the fact their positions are clearly marked on the holographic map directly in front of him.
- The smoke inside Fifield's helmet from the drugs he has put into his respirator suddenly disappears shortly after Millburn mentions it.
- When David first activates the holographic Engineers in the stellar cartography room, he is sitting in the chair facing forward. In the very next shot, when the Ghost Engineer first enters the room, David is suddenly turned to his right.
- The door to the MedPod room is already partially open when Shaw arrives (seen on the left of screen). It then starts opening completely before Shaw has finished entering the code on the keypad.
- There is a major continuity problem surrounding the fates of several mercenaries when the mutated Fifield attacks the Prometheus. This attack originally took place later in the movie, when Weyland goes to see the Last Engineer, and as a result of the sequence being moved to its position in the finished film several background characters have incongruous appearances:
- Sheppard is supposedly killed when he is flung violently against one of the transports in the hangar. However, he reappears seconds later, alive and well, driving the transport that reverses over Fifield and crushes him. Sheppard then drives off onto the surface of LV-223, and is never seen again.
- Corporal Jackson survives the attack and is seen escaping in the transport with Sheppard. Yet he later appears in the room with Weyland as Shaw walks in. Jackson even helps Shaw up onto a chair.
- Furdik is also apparently killed by Fifield with an axe when he tries to escape in the transport with Sheppard and Jackson, but he also reappears in the room with Weyland later in the film, helping Shaw up as she stumbles into the room.
- When Vickers meets with Weyland in his room, her hands are clasped behind her as she enters the room and in any shot from behind, but in all shots from her front her hands clasped in front of her.
- After leaving his room, Weyland and several mercenaries are seen walking down a hall. At first, Jackson is seen walking far ahead of Weyland, yet in the next shot he is directly behind him.
- As the group is getting into their survival suits before going to make contact with the Last Engineer, Shaw is talking to David and bends over in pain. The camera then cuts to a wide shot, where Shaw is suddenly upright before bending over again.
- On the holographic blueprint of the Juggernaut, it is clearly shown that the three entrances located near the craft's center lead directly into the pilot chamber (as was the case in Alien). Yet during all the subsequent scenes set in the chamber, there are no doorways to be seen.
- When the Prometheus collides with the departing Juggernaut, the close up of the impact shows devastating damage which results in a massive explosion and fireball. However, as the Juggernaut falls to the ground there is no sign of any damage from the collision or explosion in the area where the Prometheus hit it.
- After the Prometheus crashes, Shaw barely makes it to the escape pod with less than 30 seconds of oxygen remaining in her suit. After her confrontation with the Last Engineer, she leaves again without ever refilling her supply.
- The inside of the life boat is a mess following its crash-landing on LV-223's surface, with books and other objects strewn across the floor. Yet there is a bottle of vodka sitting perfectly upright on the bar in the background. (In fact, this goof was actually created by the removal of a deleted scene, in which Shaw goes to the bar, removes the bottle from the holder it is securely stored in, then places it on top after taking a drink.)
- Shaw is carrying an axe when she enters the escape pod, but when the Last Engineer attacks her it is suddenly gone. A sound effect of it hitting the floor can be heard, but Shaw's hands are clearly empty before the Engineer even reaches her. Originally, Shaw's fight with the Engineer in this scene was longer and she used the axe against the creature, but the scene was cut, making it seem as though the axe simply vanishes.
- If the atmosphere on LV-223 is unbreathable, the Last Engineer should have decompressed the life boat when he forces his way on board in pursuit of Shaw. While the pod's atmosphere may well have been able to replenish itself almost immediately — indeed, it does this after Shaw first climbs aboard — the process would at the very least have been noticeable, especially as it seems unlikely the Engineer would have patiently used an airlock to enter (a deleted scene confirms this, showing the Engineer forcing the doors open rather than operating them properly).
- The hair on David's severed head repeatedly changes between being neat or messy when Elizabeth is carrying him around.
- Shots of the Deacon alongside the Last Engineer show that it is too large to have realistically fit inside the Engineer's abdomen.
- During his holographic briefing, Weyland points out that he will be dead by the time the crew see the recording, when in reality he is secretly stowed away aboard the Prometheus with them. However, given that his plan involves being revived from hypersleep once a living Engineer is found, this subterfuge will inevitably be revealed, rendering the entire deception pointless.
- Immediately upon discovering a breathable atmosphere within the Engineer structure, Holloway brazenly pulls off his helmet, despite the fact there could be any number of potentially lethal alien pathogens or organisms in the air that human scanners simply do not have the ability or knowledge to detect. When he shows no immediate signs of being affected, the rest of the team promptly join him in removing their helmets as well, despite the fact they were pointing out how ridiculously unsafe his actions were just moments before, and ignoring the fact that it could conceivably take minutes, hours, days or even weeks for any alien contagion to have a noticeable effect on Holloway's health. Supposedly expert scientists would never be so reckless in their position.
- Fifield and Millburn get lost inside the Engineer Temple, despite the fact the former is supposedly the team's mapping expert. Moreover, the rest of the team are perfectly capable of finding their way out, even when frantically fleeing the temple ahead of the incoming storm, yet the two lone scientists are incapable of finding the exit.
- Millburn and Fifield elect to leave the Engineer Temple because they become frightened by the potential presence of possibly dangerous alien creatures, yet when they later discover the Hammerpede, Millburn immediately and gleefully attempts to touch it, despite the fact the creature is quite obviously acting aggressively at the time. Once again, this is something an expert biologist would never do — especially when dealing with an extraterrestrial creature that has never before been encountered by mankind (nor encountered mankind itself).
- Vickers states that she has no interest in Weyland's mission to find his creators and extend his lifespan, insisting that all she cares about is taking control of his company once he is dead. If that is the case, why has she joined a very lengthy and in all likelihood hazardous mission into deep space, simultaneously placing herself at risk and giving her corporate rivals on Earth several years to plan their ascension to head of Weyland Corp in her absence?
- David infects Holloway with the black liquid for seemingly no reason other than curiosity, despite the fact doing so could well be hazardous and could even threaten the safety of Weyland, whose survival David is supposed to be ensuring.
- As Weyland and his men prepare to leave the Prometheus in search of the Last Engineer, Shaw staggers into the room covered in blood and in obvious physical distress, yet no one shows any concern for her nor even enquires as to the cause. Even if Weyland's people were totally indifferent to her suffering, the mercenaries assigned to protect him would at least want to know what had caused her condition, in case it has implications for Weyland's safety. Given that the ship has already been attacked by the mutated Fifield, their lack of concern towards a potential threat is especially baffling. Perhaps most confusingly of all, even David shows no interest in what has happened to Shaw — and the organism that he knew was growing inside her — when previously he attempted to have her put immediately into stasis after discovering the creature.
- The film implies that the Engineer complex on LV-223 was a research facility developing powerful biological weapons. If this is indeed the case, why did Engineers in ancient times leave humanity a map leading to a biological weapons depot, especially if they ultimately intended to return to Earth with those weapons and wipe mankind out?
- Vickers is crushed to death when the Engineer ship crashes because she runs along its falling length in a straight line — yet if she had simply run to either side, the shape of the ship means it would have missed her. In fact, Shaw is able to avoid the ship simply by rolling to one side on the floor.
- After the Sacrifice Engineer drinks the black fluid and disintegrates into the river, you see his DNA floating in the water. However, this would be impossible. In terms of size, DNA is at the molecular level; in other words, one should only be able see his DNA floating amongst other H2O molecules.
- Primitive artwork created by ancient man, in some cases no more than a crude painting scrawled on the inside of a cave, could not possibly be detailed or precisely accurate enough to uniquely identify one star system some 35 light years away from Earth.
- In the scene where Holloway exhibits the ancient artifacts that depict the star system they are travelling to, he shows artifacts from Sumer, Babylonia, Mesopotamia and Ancient Egypt, and refers to these as "unconnected" cultures. In fact, the terms Sumer and Babylonia both refer to Mesopotamia (in the region of modern day Iraq); the terms Sumerian and Babylonian are generally used to refer to different time periods in Mesopotamian history. These three terms actually refer to the same culture, and so they are far from unconnected. Furthermore, it is well known that the people of Sumer/Babylon had extensive contact with the Ancient Egyptians via trade and war.
- The Prometheus travels approximately 35 light years to reach LV-223. Vickers comments they are half a billion miles from Earth, yet half a billion miles is barely farther than Jupiter, and nothing like the distance to another star system.
- Ford states that the atmosphere of LV-223 is lethal to humans due to its carbon dioxide content of 3%. In reality, CO2 is not lethal until the concentration reaches 7% or more.
- Following the operation to remove the infant Trilobite from her stomach, Shaw spends the rest of the movie running and jumping around. While she acts as though she is in pain, this kind of behaviour would be totally impossible following such invasive surgery. In fact, the MedPod apparently only superficially stapled her wound together and did nothing to repair the internal damage and incisions, and as such Shaw would almost certainly die of internal bleeding fairly quickly, even without physically exerting herself.
- The Juggernaut is flying away from its launch site when Janek crashes the Prometheus into it from behind, yet after the impact the Engineer ship falls back to where it started, landing almost directly on top of Shaw and Vickers near the hangar. This goes against basic physics — in reality the ship's forward momentum at the time of impact would cause it to continue to travel onwards, away from Shaw and Vickers, at least initially. While its weight might cause it to crash back down to the surface quickly, it would still travel in some kind of forward arc following the collision, and it certainly wouldn't reverse course 180 degrees and head back in the direction from which the impacting Prometheus came.
- Just before the Prometheus lands, Holloway jumps up from his seat for a better view. As he does so he knocks his chair, revealing that it is not attached to the floor (which, for obvious reasons, would be an incredibly unwise design choice on a spacecraft).
- The spacesuits worn by the crew when on the surface of LV-223 have the wearer's EKG readings (heartbeat) projected inside the helmet as part of a head-up display. However, this heartbeat reading is identical for all of the crew members and never changes in response to the altering stress levels they experience.
- When Fifield shines his torch over the dead Engineers he and Milburn find, the arm of one of the corpses can be seem wobbling, showing it to be made of rubber.
- When Shaw places David's head into the bag, the footage has been flipped as the camera on Shaw's suit is suddenly on her right shoulder, not her left as at every other point.
- ↑ "Weyland-Yutani Archives - Prometheus: The Lesser Known Deleted and Alternate Scenes". Retrieved on 2013-11-21.