Ass Pull: Kyurem is able to change into its Black or White Kyurem forms at will, and can even switch between the two, without needing to absorb Reshiram or Zekrom like it has to in the games. The only explanation you get is how it can "harness their powers" due to being born at the same time as them, but not much more beyond that.
Broken Base: While the movie is regarded as one of the better Pokémon movies by fans, there are those who dislike it for various reasons, such as the overabundance of telepathy-using Pokémon (of the five Legendary Pokémon featured, all of them use telepathy), the shorter-than-average runtime, a somewhat thin plot and the Pokémon outshining the humans to the point of rendering their inclusion unnecessary. There are those who actually like the Pokémon overshadowing the humans, the incrwased emphasis on characterization of said Pokekon, and the character development a good chunk of the cast gets over the course of the movie. Overall, fan opinion is basically split between those who were pleasantly surprised by the movie and those who still found it lackluster.