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)
The Silver Surfer & the Coming of Galactus: Part 1 - S1-E5
Continuity mistake: When Reed is stretching up to speak to Galactus, the black 4 on his chest briefly turns white. (00:20:04)
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.
And the Sea Shall Give Up Its Dead - S1-E1
Continuity mistake: When Iron Man and War Machine are battling Titanium Man, they each grab one of his legs and flip him on his back, with the two shown to be standing near his feet afterwards. The shot then changes to show Iron Man jumping towards Titanium Man, even though he was already standing right by him. When the shot changes again, Iron Man is at Titanium Man's feet, but War Machine is nowhere to be seen.
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)