Revealing mistake: During the brief firefight in the mess hall, Distephano is disarmed and drops to the floor. After the firefight, he surrenders and stands up with his hands behind his head. The same shot of him standing up is reused in the security footage Gediman watches from the control room seconds later. (00:39:05)
Other mistake: When Ripley pulls the knife out of her hand the blade is smoking as her acid blood is melting the steel, however shortly after she touches the girls face and hands, and the acid blood has no effect.
Factual error: In reality, the normal air pressure of a room (about 14.7 psi) would be nowhere near enough to force the newborn's body out through such a tiny hole.
Audio problem: In the nest, the creepy guy talking does not sync his words with his lips half the time.
Visible crew/equipment: When the android is connecting to the ship, in a lot of close ups what looks like a stage lamp is reflected in her eyes. There wasn't anything in the room that looked like that.
Continuity mistake: The scene when the surgery is performed to remove the baby alien, in the first shot shows the laser cutting below Ripley's breast area. In the next shot you can see the shape of her left breast under the surgical protective material.