Continuity mistake: When Thrax enters the Hypothallimis, he kills one scientist, he then attacks the other scientist wearing glasses. When he picks up the scientist's glasses, there is tape holding them together in the middle, but when the glasses land on the ground, there isn't anything on the glasses at all.
Continuity mistake: When Frank drops his egg, it is almost all clean, but when he gets it up, it is dirty.
Audio problem: In the scene "By The Throat", After Osmosis goes down the escalator. The red air stuff starts to go around them. Osmosis moves his mouth but not until a couple seconds later when the shot changes do you hear what is that cherry stench. (00:20:37)