Revealing mistake: When Newt is sliding across the grated floor, Bishop reaches out to save her and you can clearly see he's standing in a hole to make him look cut in half.
Continuity mistake: When the Marines first enter the reactor room, the "Mission Time" readout on the shoulder mounted cameras jumps backwards and forwards in time with every cut.
Continuity mistake: In the sequence when the APC is fleeing the hive, and the alien punches a hole though the windshield to get to Ripley. The hole disappears in the next shot when the light reflects off of the glass.
Continuity mistake: There are many holes in the 'squad structure' once the marines arrive at Hadley's Hope. Gorman calls up 1st Squad (comprised of Apone, Vasquez, Crowe and Hudson) to approach the colony first. They do. But, if you look closely, there are other marines present. When they arrive at the door Apone goes straight to the console, Hudson holds back to our left and Crowe rests in the background on the right of the screen. Apone then calls Hudson up to do a bypass. If you look closely as Hudson runs up to the console you will see Frost in the background, he steps up to the left of Crowe (his left) and on the left of the screen, you will see Wierzbowski crouch with his flamethrower, slightly obscured by Vasquez (look between her legs). Then 2nd squad is called up. It is comprised of Hicks, Dietrich, Drake, Frost and Wierzbowski. Watch the shot of Vasquez entering the lock and you will see Frost standing roughly where he was when the 1st Squad ran up. Clearly the original scene had all the marines descend on the North Lock simultaneously. The confusion continues when Gorman, Ripley, Burke and Bishop enter the South Lock. They meet up with Hicks' squad yet Dietrich and Wierzbowski are curiously absent.
Continuity mistake: When Ripley and the Queen fall into the airlock, look closely at the Queen's tail. It seems that the sharp end of it is broken off, or missing. Later on in that scene it is back.
Revealing mistake: In the Special Edition of the film, in the scene where the Marines are conducting their initial search of the colony, the shot where Hudson and Vasquez enter the "negative situation" room (where they find the hamster) is obviously sped up. You can tell by how quickly Vasquez seems to move when she comes through the door.
Other mistake: When the autoguns fire at the aliens for the second time, there is a flashcut of an alien being blasted apart. Watch closely; it's the same clip of the alien that Vasquez shot and subsequently sprayed Drake with acid.
Continuity mistake: In the end of the film, when Ripley pulls the Alien queen down in to the hatch we can see that the bulb on top of the machine cracks but when they are lying on the hatch the bulb is whole.
Continuity mistake: You may need slo-mo to see this: towards the end of the film, when Ripley is going down in the elevator to save Newt, pay close attention to the indicator screen counting off the floor numbers as they pass by. It goes floor 8, 7, 6 then 7 again and then 5.
Continuity mistake: During the scene where Ripley is trying to break the window with a chair, there is a scuff mark on it before she hits it. It goes away and comes back.
Continuity mistake: As the marines first enter the med labs, Drake at the front, there are some neon tubes hanging from the ceiling that slowly rotate to face the camera. As the angle changes and Drake goes round a corner, the neon tubes rotate to face where the camera previously was again in the background.
Revealing mistake: Right before Ripley discovers all of the eggs that the Alien Queen has laid, look at Newt's fingers as Ripley is carrying her - It's obviously a fake hand. Newt is in fact a dummy in this scene, and others preceding the chase from the Alien Queen. This dummy was created so that Weaver would not get exhausted carrying a real child around for so many scenes/takes.
Continuity mistake: When remote sentries A and B start firing at the aliens in the tunnel, the display on A shows 500 rounds before they start firing. However, both remotes A and B had been previously test-fired by Vasquez and should show lower counts.
Continuity mistake: Director's cut: When the autoguns were mowing down the army of Aliens coming through the service tunnels, there should have been enough acid blood being sprayed out to melt a massive hole in the tunnel. But the acid has no effect at all on the tunnel walls.
Continuity mistake: During the Cargo Loader vs. Queen fight, Ripley grabs the Queen and it closes around her neck. In the next shot it is closed around its head. It changes extremely quickly; therefore it couldn't have changed position.
Continuity mistake: When Ripley and the marines go to where the colonists are, there is a ladder in front of the vehicle that was driven inside; the ladder would be in the way if the vehicle was driven further in. But when all hell breaks loose and Ripley decides to drive the vehicle further in, to rescue the marines, the ladder is gone - in fact, a lot of things look different the second time round.
Continuity mistake: Just before the marines are extracted, Hicks tries to close the APC door. An alien stops the door and tries to get inside. Hicks picks up his shotgun and jams the muzzle into the alien's mouth and fires, killing the alien. The alien falls away, they immediately close the door and the APC begins to back up. The camera shot changes to an outside view of the APC. If you look at the area as the APC backs up, you'll see falling debris but no dead alien. It's doubtful the marines would've pulled it into the APC as we don't see it again, or that they would've kicked the corpse out really far due to the acid.