Aim to Be a Metamon Master! Imite - S4-E17
Revealing mistake: At the beginning of Team Rocket's motto and shortly after, James appears to be floating in midair. (00:06:49 - 00:07:30)
Aim to Be a Metamon Master! Imite - S4-E17
Revealing mistake: When Pikachu joins the fight against Team Rocket, he passes through Mini-Dit. (00:15:51)
Goodbye Chicorita!? The Electric Labyrinth! - S4-E42
Revealing mistake: After Team Rocket enters the lift, Ash runs in place for a few frames in the transition to the next shot. (00:16:42)
Answer: He is a good guy but just found himself in a bad situation when he worked for Lysander. He didn't want him to harm Ash and his Pokémon when he was trying to get the special bond between Ash and his Greninja to work. He does leave Lysander and go back to being a good person.