Mewtwo VS Shadow the Hedgehog - S3-E6
Revealing mistake: During Shadow's Super Shadow transformation, half of the background becomes a green screen.
Nightwing VS Daredevil (DC VS Marvel) - S5-E12
Nightwing: What are you?
Daredevil: Better. (00:16:10)
Trivia: This was the first episode of the show with actual voice acting.