Pokémon, much like real-life creatures, need to be trained in a certain manner and discipline in order to properly master said Pokémon. In the games, whenever a trainer levels up and evolves a Pokémon too quickly, the Pokémon stops listening to him due to the fact that that the Pokémon has surpassed the trainers level of experience, therefore not finding themworthy of listening too. It isn't until the Pokémon reaches level 40 that it masters the discipline to listen to its trainer, should it reach its final evolution too quickly.
In the Pokémon anime, it is Ash's dream to become a Pokémon Master, a title which has yet to be fully explained, but most likely involves mastering the art of training Pokémon. However, throughout the series, he occasionally comes across the problem of disobedient Pokémon. This was especially true during the first season of the series when Ash was considered an amateur trainer and had little experience to match his Pokémon's skill level.
10 Pikachu - When It Refused To Get Inside Its Poké-Ball
The story of how Ash met Pikachu is a classic tale amongst Pokémon fans, seeing as Pikachu was Ash's very first Pokémon, ever. So it's no surprise that Pikachu, being a very powerful Pokémon in its own right, didn't respect Ash very much when they first met.
Pikachu refused to get inside a Poké-Ball during their first encounter, which forced Ash to walk with it on a leash. Not to mention, Pikachu consistently electrocuted Ash and anyone in their vicinity, without Ash's consent. The Electric-Mouse Pokémon even mocked Ash when he failed to catch a Pidgey.
9 Pikachu - When it Didn't Want To Battle Misty
During the episode, The Water Flowers of Cerulean City, Ash and the gang reach Cerulean City, where Misty reveals she is one of the four Gym Leaders of the Cerulean City Gym, which specializes in water-type Pokémon.
When Misty challenges Ash to a battle, he originally chooses to send out Pikachu, who's electric0type moves would give Ash an advantage over Misty's water-type Pokémon. But surprisingly, Pikachu refuses to go to battle, expressing to Ash that it simply doesn't want to fight Misty, since it considers her a friend.
8 Charmeleon - When It Went All Out Against Paras
After evolving from Charmander, Ash's Charmeleon became his strongest Poké, which made sense why it didn't listen to Ash, who was still an amateur trainer at the time. In episode 44 of the original series, titled The Problem With Paras, Charmeleon refuses to loose against a weaker Paras, even if it was a fake battle, lighting up Ash with a flamethrower attack, and attacking the weak Paras.
It is then explained that Charmeleon's skill level had far exceeded Ash's own skill levels, and it could not respect Ash as a result.
7 Charmeleon - When Ash Was Attacked By Prehistoric Pokémon
In episode 46 of the original series, Attack of the Prehistoric Pokémon, Ash and Team Rocket fall into a cave-pit filled with wild prehistoric Pokémon that have been living underground cave system. When the group of prehistoric Pokémon - composed of Kabutos, Kabutos, Omastar, and Omanite - begin to attack Ash and Team Rocket, Ash sends out it's Charmander to defend them.
But after viewing the Prehistoric Pokémon, it thinks they're too boring, and proceeds to take a nap on a rock while the prehistoric Pokémon chase Ash and Team Rocket all over the cave.
6 Charizard - When It Almost Cost Ash A Gym Badge
During his first Gym battle against the Cinnabar Island Gym Leader, Ash sends out his Charizard against Cinnabar Island Gym Leader, Blaine, after Blaine's Ninetailes knocks out Ash's Squirtle. Blaine switches out his Ninetails for a Rhydon, hoping to have a type advantage against Charizard, but the Flying-Fire type simply takes off into a corner of the Cinnabar Island Gym and begins to take a nap.
As a result, Blaine disqualifies Charizard from the battle, which almost cost Ash the Gym Battle later on, when he lost.
5 Charizard - When He Refused To Fight Sparky
In the midst of a battle against Ritchie during the fifth round of the Indigo League, Ash finds himself on the ropes against Ritchie and his Charmeleon, Zippo. Ash, not having any other options, sends out Charizard, who instantly scares Zippo into being recalled. After Ritchie sends out his Pikachu, Sparky, Charizards scoffs at it and proceeds to take a nap in the middle of the battle.
Ash orders and begs Charizard to get up, but it refuses to listen to Ash, costing him the battle and the Indigo League altogether. This is the first time a Pokémon's disobedience cost Ash a major win.
4 Charizard - During A Battle Against Polywrath
While on the Orange Islands, Ash battled Tad, a trainer who had previously fought against the Trovita Island Gym Leader, and heard of Ash's strength. Ash had sent out Charizard against Tad's Polywrath after Polywrath had defeated Pikachu in battle. But rather than listen to Ash, Charizard began using his Flamethrower attack against Polwrath, with no effect due to Polywrath being a water-type.
Despite this, Charizard kept blasting Polywrath and ignoring Ash's commands. Polywrath then uses an Ice-Beam attack, which completely encases Chariard in ice.
3 Charizard - When It Tried To Burn Down A Village
After arriving at Mandarin Island, Ash is encouraged to battle against another trainer after being ignored by Prima, a Pokémon Master. He finds a boy who is willing to battle and challenges him. After a while, the boy sends out his Taurus, while Ash sends out Charizard, but Charizard easily defeats the Taurus. Charizard then flyes off and begins to set fire to the local village while on a Rampage.
When Ash attempts to call Charizard back, the flying-fire type Pokémon doges the Poké-Ball beams, forcing Prima to get involved.
2 Froakie - When It Attacked Fletching
Ash's Froakie was always a bit of an independent loner at the beginning of the Pokémon: XY series, seeing as how repeatedly left its trainer or was returned to Prof. Sycamore because of its disobedience. While on Route 4 with Ash, a Fletching stole a berry from Bonnie's hand, making her sad in the process.
Froakie took the act personally and began to attack Fletching, but continually missed his hits. Ash tried to order Froakie to stand down, but Froakie disobeyed him and continued to attack Fletching, despite continually missing his hits.
1 Lycanroc - When Its Fur Got Dirty And It Started To Attack Aimlessly
After evolving from a Rockruff, it was revealed that Lycanroc would go berserk and lose control whenever it dirtied its fur or mane, of which it was very proud. This was first revealed after Ash's Litten accidentally dirtied Lycanroc's fur, causing it to attack Litten.
It doesn't become obvious what a problem this was until a battle with Gladions Type: Knull, when Lycanroc was thrown into a nearby pond in the midst of an attack. This caused Lycanroc to become enraged and attack Type: Knull aimlessly, ignoring Ash's commands and just charging on its own.