If a Pokémon listens to its trainer, it is called an obedient Pokémon. But there are cases when a Pokémon doesn't listen to its 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 badges they have.
In the anime
This is also carried into the anime as well. The main cause of Pokémon disobeying a Trainer is different for each, but it mostly stems from a Trainer being unable to control their Pokémon, most notably Ash's Charizard because it evolved at a rapid pace which would be hard for a new Trainer to control.
Pokémon which weren't or aren't obeying their trainers:
- Ash's Pikachu
- Ash's Charizard
- Ash's Primeape
- Misty's Psyduck (not purposefully)
- Otoshi's Marowak
- Ash's Corphish
- Guy's Loudred
- Dawn's Mamoswine
- Dawn's Buizel (obeyed Ash)
- Iris' Excadrill
- Iris' Emolga
- Luke's Zorua
- Bianca's Escavalier
- Iris' Dragonite
- Ash's Froakie (before joining Ash)
- Jessie's Mimikyu (unless if its fighting Ash’s Pikachu)
- Ash's Lycanroc (before learning on how to control its rage)
- Misty's Gyarados