The Pokémon games and anime may have worked well to get this storied franchise to the heights it currently finds itself at, but that doesn't mean that they have always stayed consistent and worked well together. In fact, there have been plenty of occasions when the anime has neglected or broken significant rules that the Pokémon games established.
10 Gameplay Rules the Pokémon Anime Always Ignores (& Why)
Pokemon games have some rules that the anime doesn't follow. However, there are usually good reasons for this.