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.
Audio problem: After Sarris' first missile has hit the ship, Jason runs towards Tommy and shouts, "Tommy, let's go, get us outta here, go go go go go." However, what we hear is not in sync with Jason's mouth until the last 'go'.
Audio problem: In the early backstage scenes from the convention, the other actors are angry at Tim Allen's character. The actor who plays Laredo clearly says "You are so full of sh*t", but it is edited to "full of it." Those two word edits ('s' word and 'f' word) were done to keep the PG rating, but the editing is sloppy. [This theory could also be expanded to the drug reference mentioned above].
Audio problem: When the aliens are talking to Taggart at his house, in a shot from behind the aliens looking at Taggart in the doorway, the audio is out of sync with the alien leader's mouth. You can see this when he says the word "destruction."
Audio problem: When Brandon's parents are listening to the news reporter talk about the crew not showing up to the convention, his words don't match his mouth at the end of the shot.
Audio problem: When they are rolling the beryllium sphere into the ship, Laredo is heard yelling, but his mouth isn't moving.
Audio problem: Right after the Thermians become sad over the mention of Gilligan's Island, Alexander rolls his eyes and starts to turn away, while you can hear him saying "Oh brother." However his lips are not moving for this indicating the line was dubbed in.