1. Don't Nickname After Shitty AnimeMany people tend to make this mistake when starting out. For example, the Buncha Bulls' very own Snake nicknamed his Aegislash after Asuna, but doesn't recognize Sword Art Online for the garbage that it is. Generally, you'll want to avoid naming your precious Pokémon after anime that you should be avoiding: such as Naruto, Sword Art Online, Shingeki no Kyojin, etc.
Nothing makes me cringe more than seeing a poor Tyranitar or Hippowdon being named 'Gaara'. It's not the Pokémon's fault here, the trainer's poor taste is to blame.
2. Your Nickname Choices Have To Make Some SenseThis isn't as much of a common problem as the first rule, but still something to keep in mind. Naming your Pokémon after somebody some to make at least some kind of logical sense that doesn't require too much explaining. For example, naming your Kingdra after Kamijou Touma from To Aru Majutsu no Index makes absolutely no sense since Kingdra is seahorse while Touma is known for breaking illusions and punching bitches. However, nicknaming your Kingdra after Misaka Misuzu would make more sense because they're both drunk.
Nicknames shouldn't be restricted to characters either—you can use attacks or special moves as well. For example naming a Gardevoir after Shokuhou Misaki's Mental Out works.