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
Revealing mistake: When Mary Jane and the other servants of Baron Mordo are flying through the city, they literally disappear into thin air. Probably a problem with rendering the 2D animation within the 3D animation. (00:01:00)
The Accident - S1-E1
Visible crew/equipment: When Alex goes into the garage for the first time, a camera and camera operator can been seen reflected in the saw.
The Meeting - S1-E1
Continuity mistake: When Lisa and Ray are talking in Lisa's apartment there is a soda bottle on the table. Part way through the scene a cap appears on the bottle and then is gone in the final shot.
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.