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.
Neogenic Nightmare Chapter 4: The Mutant Agenda - S2-E4
Continuity mistake: When Spider-Man is battling the X-Men, he shoots webs at all of them, which they remove. Later when Spider-Man is in Xavier's study with the X-Men, Gambit is shown removing a piece of webbing from his right arm, even though he had already removed it earlier. (00:02:15 - 00:04:30)
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.