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 actual laser beams are (barely) 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.
Continuity: When Boiler and Pinback are fighting in the corridor, the gun that Boiler dropped at the beginning of the fight is on the deck not far in front of them, but when they stop fighting and climb the ladder back to the control room, the gun is not there.