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.
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.
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.
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.
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.