Revealing mistake: When he's attacked in Down Below, Dr. Franklin is shoved against a station bulkhead/wall that wobbles when he hits it. (00:15:30)
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)
Behold, a Distant Star - S2-E10
Revealing mistake: When the Fantasticar is beamed to the Skrull home world, the edge of an animation cel is visible on the right side of the screen in the shot of the beam shooting out of Earth. (00:15:26)
The Defection of Hawkeye - S1-E8
Revealing mistake: When Hawkeye is saying "Hey, what's shaking, gang?", the screen is shaking from left to right, likely indicating a composite shot. (00:08:54)