Continuity mistake: When the class is in Arnold's esophagus, Tim says something, then it cuts back to Ms. Frizzle. Arnold is sitting in the back seat of the bus.
Behold, a Distant Star - S2-E10
Continuity mistake: When Franklin Storm is telling his children not to cry, Sue is stroking his hair with her right hand. When the shot changes, her right hand is resting in front of her right leg. (00:14:08)
Neogenic Nightmare Chapter 5: Mutants Revenge - S2-E5
Continuity mistake: When the Hobgoblin crashes his glider into the railing, the entire glider is outside the railing's crossbar. When the shot changes, the glider is suddenly stuck between the gaps in the railing. (00:11:10)
Continuity mistake: After Century restores gravity to the vessel, he is suddenly nowhere near the control panel he used to accomplish the task. (00:18:06)
Continuity mistake: To beat the traffic, Coop skateboards inside a construction pipe. The pipe is on the back of a truck, so it's not exactly very long, and gets picked up by a crane arm mounted on the truckbed itself. However, Coop takes ages to come out of the pipe, and in the shot from inside the pipe it looks as if is dozens of meters above the street level, which isn't. (00:08:00)
Coach Fussell's Lament - S2-E5
Continuity mistake: Chairface and Chrome Dome arrive at the Brianchild's house in the same car, but drive off in separate cars.