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 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.