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Starscream VS Rainbow Dash - S1-E17
Continuity mistake: Rainbow Dash catches Star Scream in a tornado and spins him around so fast in his jet form that you see one of his wings break off and fall away. He plummets to the ground and transforms into his robot form and begins to beg for his life. He suddenly has both wings again at this point.
Nightwing VS Daredevil (DC VS Marvel) - S5-E12
Nightwing: Hah, see you in Hell. (00:17:40)
Trivia: This was the first episode of the show with actual voice acting.