- Continuity: Dillon's glasses disappear after Golic frees the alien.
- Continuity: When doing the autopsy, Clemens's bloodstain frequently changes.
- Factual errors: When Murphy finds the alien's shed skin in the pipe, he holds it up and it blows away from the fan. Mr Clemens also says that the fan was blowing. However on the close-up shot of the fan, the blade angle and the direction of rotation would mean that the fan would have been sucking like an extractor fan. The fan should have blown the other way, and there would be no ambiguity over the cause of Murphy's death.
- Revealing mistakes: When Dillon and Ripley are luring the alien in to the mold, Morse is in charge of shutting one of the last doors before it kills him. On slow-mo (DVD) you can quite clearly see, he does not actually hit the button he is aiming for and thus the door would not close.
- Continuity: In the cafeteria, Ripley's glass of orange juice goes from half full to full.
- Audio/visual unsynchronized: After Morse closes the channel door, trapping the alien in the piston chamber, he hollers "I'm going for the lead!" out of sync with his moving lips.
- Continuity: When Ripley says to Dillon that she has an egg inside of her and that he has to kill her, during the discussion his glasses is on top of his head. Just before he's about to deliver the kill, his glasses are hanging on his shirt. After the short "fight", when Dillon leaves, his glasses are back on top of his head.
- Continuity: When the EEV report is being made at the beginning of the film, Ripley is listed as "LT." - lieutenant. Yet, Ripley's rank was always a warrant officer, a lower rank than lieutenant (the extended inquest of the Director's Cut makes this clear). While it's true that Burke promised her that she'd be reinstated as a flight officer, since they never returned to Earth it is unlikely that this occurred, and certainly not at a higher rank than she was prior to her return to LV-426.
- Continuity: Early in the film the interior of the EEV is a mess, having been smashed up by the crash. However, as the movie progresses, it seems to be in a better and better condition and at the end it seems to be almost intact.
- Revealing mistakes: During Newt's autopsy, there is a notable amount of blood. Corpses do not bleed; once the heart stops pumping, all blood pools in the lowest parts of the body.
>>> WARNING: Here Be Spoilers <<<
Goofs below here contain information that may give away important plot points. You may not want to read any further if you've not already seen this title.
- Continuity: SPOILER: During the scene where Ripley searches for the alien in the service area there is an object in the background that is clearly an alien head. When she crushes it, it is just a curved metal pipe full of bugs despite the fact that the crushed object is in the same place as the alien skull had been.
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