If a Pokémon listens to its trainer, It is called an obedient Pokémon. But there are cases when a Pokémon doesn't listen to it's trainer, this is called disobedience.

In the games

The Pokémon won't obey the trainer if the Pokémon is at a very high level and the trainer doesn't have enough badges to train it. This is done so that players won't transfer a high-leveled Pokémon from another game and beat the game. Having all eight badges makes all Pokémon obey a trainer. In the generation three games, Mew and Deoxys which were not met in a fateful encounter will always disobey the trainer, regardless of the number of the number of badges they have.

In the anime

Pokémon sometimes do not obey their trainers in the anime too. This disobedience is not due to having enough badges, it is because the Pokémon may not trust you or respect you. This disrespect is usually overcome by emotionally appealing the Pokémon or by an act of selflessness.

Pokémon which weren't or aren't obeying their trainers:

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