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 Sue is talking about her father going into hiding, the camera is on the right side of a photo album, showing a newspaper clipping of him being wanted for murder. When the shot changes, the contents of that page are now three different photographs. (00:07:32)
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)
Rejoice! I Am Ultimo Thy Deliverer - S1-E2
Continuity mistake: For most of the episode, Ultimo is between two and three stories tall. At the end when Spider-Woman is in the lab, Ultimo is shown to only be around ten to twelve feet tall.
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.
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)