>>46102350Its mentioned in Black and White 1 & 2 that Pokemon are free to do whatever they want, they are not servants to their trainers. In fact they regularly escape abusive relationships they don't like. They also state explicitly that Pokeballs don't have any ties to making the Pokemon have to listen to you, if you capture them and they find they don't like you, they just escape the ball and leave.
If you seen the anime this happens a decent chunk with Pokemon just leaving trainers for one reason or another. I distinctly remember this with Ash's Froakie leaving his prior trainers because he didn't feel they were strong enough for him until he met Ash and stayed with him.