I mean, why would pokemon be on the side of team rocket or whatever other villainous (often apocalyptic) group the games have? They just follow whoever catches them no matter what.
Why wouldn't they? Team Rocket/MagmAqua/Galactic/Plasma/Flare all have pokemon fighting with them. They listen to the trainer, not the moral obligation of the society.
Pokemon in all versions of Pokemon are literal slaves. They have no free will if they are in a Poke Bowl. And depending on the movie - that free will can be overwritten again by a Psychic Type Pokemon.