Revealing mistakes: During the elevator sequence, which was actually shot horizontally in a corridor, you can occasionally see the plank on which O'Bannon was lying.
Revealing mistakes: In one shot in the airlock, the "laser beams" were not printed in, but the hold-out matte where they were supposed to go is visible.
Continuity: When Doolittle is talking to Bomb #20, the stars in the background change between shots.
Revealing mistakes: When they're chasing the "alien" through the bowels of the ship, one of the poorly lit rooms is actually a basement. You can see the conventional lightswitch and the conduit on the wall.
Continuity: Just before bomb #20 explodes, Pinback takes off his earphones, but they are back on a second later.
Audio/visual unsynchronized: When Pinback says, "Now it's time to go sleepy-bye, you worthless piece of garbage" before shooting the alien, his mouth actually says "worthless piece of crap."
Audio/visual unsynchronized: When Boiler starts yelling to Pinback that he can use the gun to shoot the pins off Bomb #20, his dialogue doesn't match his lips at all.