Continuity mistake: When Mays, "There might be more to Pokémon than I thought," she is there, but in the next shot, she disappears. (00:11:48)
Continuity mistake: When Ash is talking about the artifact Professor Alden is holding, the button on his jacket intermittently goes from being present to being absent and then back to present. (00:12:00)
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.