Continuity mistake: During the alien's assault on the ship, one crewman is seen near the spaceship's stairs firing a weapon. However, the weapon is pointed at a forty-five to sixty degree angle - at this angle, he would hit the bottom of the ship, not the alien that is much farther out.
Factual error: At the end of the movie the cast is counting down to the explosion of the Krell furnaces. They reach zero and the furnaces explode. They see the light from the explosion just it happens. But they are 100 million miles out by then. The light would have taken over 8 minutes, about as long as light from the sun takes to reach earth, to reach the ship.