Character mistake: Some characters use the letter "s" at the end of a Pokémon's name when the plural of a Pokémon is just its name. The best example is when Pikachu says, "Roger must've sent the Greninjas to cause the car crash." Being a Pokémon himself, there's no way Pikachu, out of all characters, would say that.
Audio problem: When Pikachu has coffee cups all over Harry's office, Tim starts knocking them over. The cups make a plastic/can sound, but the cups are cardboard.
Plot hole: After Pikachu and Mewtwo begin falling down, Tim is suddenly on the ground in a matter of seconds, with little to no time to arrive there. There are multiple stairs, and he does not have any Pokémon to help him get down. He couldn't have gotten to the ground that fast.
Other mistake: In the beginning of the movie, Mewtwo is escaping the laboratory. He blows up his surroundings, then shoots up out of the containment chamber. Later in the movie, Tim and Pikachu see a holographic flashback of that same moment. Although in the hologram, Dr. Laurent is directly in front of the chamber when she wasn't in the beginning of the film.
Other mistake: At the beginning, when Tim arrives in Ryme City, a Sneasel is visible with its ears on the wrong sides.
Suggested correction: As an adaptation, the movie is allowed to alter the design of characters and creatures from the games. It doesn't need to stay 100% consistent with the game, and thus, this cannot be considered a mistake. Other Pokémon in the movie similarly have minor cosmetic changes. Furthermore, you could also easily chalk this up to the Pokémon's genetics simply being different. Natural variation or mutations happen sometimes in species, and it's canon in Pokémon that some of them have different forms or look different even if they're the same species. (Ex. I have a number of the same Pokémon that all look completely different in Pokémon Go.)
