Continuity mistake: During the opening sequence of Alexander storming out of the back rooms, you can see Tommy help keep him there. However within the next shot as they Call Gwen to the stage, you can see Tommy and the whole crew out on stage but Alexander and the Commander are still having the same dialogue. (00:04:10 - 00:05:00)
Continuity mistake: When the 4 "nerds" first approach the captain to talk about their supposed problem the girl is standing in a different place than when they cut back. In a later scene the girl is in this position and I believe they reshot the earlier scene while they were doing the later scene. (00:07:30)
Visible crew/equipment: When the crew is escaping with the beryllium sphere, there a shot where you can see the filming crew at the top left corner of the image. (00:53:55)
Suggested correction: Having watched it carefully, I can't see any film crew in shot at any point in this sequence.
Audio problem: When Commander Taggert (Tim Allen) and Lt. Madison (Sigourney Weaver) first see the hallway with the chompers, she says, "Oh, screw that!" but if you watch her lips she clearly uses the 'f' word instead of 'screw'.
Revealing mistake: When the bridge is exploding from the mine attack, the stuntman playing Jason obviously launches himself out of the captain's chair.
Factual error: Laredo drives the ship out of the starship docking station and scrapes the main hull on the walls. This would not be possible without either scraping the wings first, as they are much wider than the main ship, or turning nearly sideways, which they clearly don't.
Deliberate mistake: When Commander Taggert and Lt. Madison are about to press the blue button to stop the ship exploding, Lt. Madison's tunic is mostly zipped up. A few seconds later it is suddenly mostly unzipped. Those of you who have access to the DVD of the film can see that there was a deleted scene which was originally intended to go in here where she unzips her tunic to distract the aliens.
Continuity mistake: In the electronic store sale scene where Jason is trying to convince his cast mates to help the Thermians, a quick shot of him shows him bending very low at the table, then suddenly he is almost standing erect.
Continuity mistake: When the Thermians enter the bridge to witness the ship being taken out of the spaceport, Guy is standing in front of and above Teb, but when the shot changes, Guy is now standing behind Laredo and on Teb's right.
Continuity mistake: At the dinner table, when Mathesar is speaking about their former commander, the fork Jason holds in his left hand instantly switches position several times.
Continuity mistake: When Fred is giving Guy the "comic relief" pep talk, his left hand is on the left side of Guy's chest, but then the view changes to Guy's right side and Fred's left hand is now on the right side of Guy's chest, where it remains until Fred turns Guy and they walk out of the scene.
Continuity mistake: When the Thermians meet the crewmen in their true form, Fleegman instantly changes position from standing erect to slouching.
Continuity mistake: As Mathesar speaks to Jason by the sliding glass door, he changes position and distance from Jason and the door.
Continuity mistake: When Guy is introducing the actors at the start of the movie, while he is saying Jason's name, to the right of the screen you can see that Guy is holding a glass of water with lemon. The camera then cuts to an overhead shot of the whole crowd and Guy can be seen clapping with nothing in his hands.
Continuity mistake: When they are rolling the beryllium sphere back to the ship, Fred has his paper bag in his mouth in some shots and it disappears completely in others.
Audio problem: When Mathesar says "We need to separate or we'll die," his mouth doesn't move for "We need to separate."
Suggested correction: Your lips don't move much saying that line, especially if you have a fixed smile. His lips definitely move. He is definitely saying the line.
Continuity mistake: When Jason gets in the limo with the Thermians, the limo starts off having no license plate and changes to a California plate between shots.
Continuity mistake: At the end, when the crew is bowing to the fans, Sigourney is shown moving her right leg back a small bit. However, when they show them standing up from the bow, her right leg is fully crossed behind her.
Revealing mistake: When Saris is torturing the Thermian commander, he stops and approaches Commander Taggart; while Saris is talking to Taggart you can see the lips and teeth of actor Robin Sachs behind the mask.
Audio problem: When Gwen uses her Gilligan's Island analogy, Mathesar says, "Those poor people," and then Tommy says, "Oh brother." We are then shown Guy standing next to Gwen, and Guy says "We're screwed," although if you watch his mouth he actually says something like, "We're dead." This dub is probably for a similar reason to that of why Gwen and Tommy's swearing was dubbed over.