Deliberate mistake: The 'NNN' news program shows a picture of some animal crackers in Frank's stomach. The problem is, they are still all in one piece and are pretty big. I don't think Frank would swallow them whole.
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.
Audio problem: In the scene "By The Throat", After Osmosis goes down the escalator. The red smoke starts to go around them. Osmosis moves his mouth with no sound, but not until a couple seconds later when the shot changes do you hear what is that cherry stench. (00:20:37)
Continuity mistake: When Frank drops his egg, it is almost all clean, but when he gets it up, it is dirty.
Continuity mistake: When Frank is asleep and his temperature starts to rise after Thrax attacks the hypothalamus, he jerks in his sleep causing the half-eaten circus peanut on his pajama pocket to roll down and away. But then when he wakes up, the circus peanut is back on his pajama pocket.