Continuity mistake: Ripley kills the alien in the corridor after it has killed the first member of the Betty crew but there is no melting of decks or bulkheads from the creature's acidic blood. Also, the Betty crew seem unaffected by all the acid. (00:46:00)
Other mistake: In the scene where Ripley throws the basketball at Johner, Christie says to Ripley, "Ok, I've got a new game, tag .." He hits her with the handles straight in the face once, he misses the next shot, misses again, and Ripley hits him to the ground, but you neither see or hear the handles fall. (00:23:15)
Revealing mistake: When Hillard throws the basketball at Ripley, you can clearly see the white tape on Ripley's hand which was used to catch the ball. (00:23:10)
Continuity mistake: When the whole crew of the Betty are being arrested in the Mess Hall, Christie puts his hands behind his back to get the guns on his arms. But in the next shot when Christie is behind Wren his hands are by his sides. There's no way he could put his hands by his sides without the guns showing. (00:33:25)
Audio problem: Near the end of the film, when we see the Queen's new mutation, the scene opens up by showing all the scientists attached to the wall. Dr. Gediman is rambling on and on about the Queen's 'perfect' mutation. However, it is quite clear he isn't saying any of the words. In fact, from the way his mouth moves, it looks like he's literally saying 'blah blah blah, blah blah blah'. (01:27:05)
Continuity mistake: When Ripley is playing basketball, in the shot where Wren claps his hands, even though the exit is partly obscured by Wren and Gediman, you can see that Vriess and the wheelchair are missing behind them. (00:22:35)
Visible crew/equipment: When Call spills Jona's 'battery acid' drink, she throws the boxing gloves on the table. When she does, they bump the camera. (00:28:15)
Revealing mistake: In the underwater scene, Johner fires a grenade launcher at two of the aliens that are following him. Watch closely and you'll see the grenade pass through one of the aliens' head for a few frames without damaging it before exploding. Slow-mo might be helpful to spot it but isn't vital. It's perfectly visible at normal speed.
Continuity mistake: During the surgery, Ripley is cut in the chest, below her breasts. When Wren checks the scar, it appears between her breasts. (00:03:25 - 00:06:45)
Continuity mistake: When we first see inside the betty where Winona Ryder's character and the guy in the chair are fixing some mechanical stuff, Ron Pearlman's character throws a knife into the dead leg of the guy in the chair. Winona sees this and puts her large spanner on top of the thing she was working on to go get the knife, but you can see that the spanner slips off the thing but we don't here a loud noise of the spanner hitting the metal floor. Also, in the next shot it is back on top of the thing. (00:14:00)
Continuity mistake: In the scene when the new alien type newborn bites the scientist's head, just after killing the Queen, lots of blood comes from the hole in the guy's head. The alien gets all bloody in the mouth, but in the next shot the alien's mouth is clean. (01:31:30)
Continuity mistake: When Ripley discovers the clones, before the close-up of the door, there's a shot of everyone walking. At this point in the film, the group consists of eight people (Ripley, Call, Christie, DiStephano, Hillard, Johner, Vriess and Wren), but there are nine people walking in this shot. The extra person seems to be Purvis, who is the second person to enter the shot. The camera only shows his feet in the beginning of the shot, and when it pans up, you can see him walking in the background. The problem is, Purvis isn't found before the next scene. (00:50:25)
Continuity mistake: In the shot of Ripley smiling in her "cell" when the aliens escape, she is barefoot. After she shoots the alien, she is wearing boots, and a waistcoat that she was not wearing before. Her pants are different as well. (00:36:15 - 00:44:30)
Continuity mistake: After the newborn alien kills DiStephano, it has blood on its hand. When it caresses Ripley's face, the blood is gone.
Continuity mistake: Since when is invincibility a side effect from having a chestburster come ripping out of your chest? In all the previous movies, the victims were in immense pain and practically incapacitated, yet Purvis suddenly becomes the Incredible Hulk, gets shot almost a dozen times, and keeps on coming so he could attack Wren. Understandably, he was angry and adrenaline pumped, but those bullet wounds would have killed any human being, regardless of whether or not there was a chestburster about to rip out. (01:26:15)
Continuity mistake: When Elgyn is going down the hallway picking up the guns, he finally comes upon a pistol. When he picks it up, there is alien slime all over it, but there is nothing else around him at all. Yet when the alien pulls him through the grating, there are gibs and assorted chunks of gore all over the place, which were not there only seconds before.
Continuity mistake: When the guard discovers metal on Johner, in the shot after Johner says, "My own recipe.", the position of Call's head is different from the previous shot. (00:16:40)
Audio problem: When Dr. Wren takes Cal's gun, he says, 'You really are way too trusting', but his mouth movements seem to show him saying something else. It appears to be something along the lines of 'far too trusting,' as opposed to 'way too trusting.' (01:09:30)