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.
Sins of the Fathers Chapter 1: Doctor Strange - S3-E1
Continuity mistake: When Peter wakes up from Baron Mordo's illusion, he is wearing a monk's robe with sneakers and is barehanded. He removes the robe, revealing he was wearing his Spider-Man costume underneath, but his gloves and boots magically appear on his hands and feet as well. (00:09:45)
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.