Asspull: 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.
Freud Was Right: Very much so with the metaphorical 'swords' the Swords of Justice summon, and Keldeo's attempt to summon a sword of his own with his feelings to it not helping. The scene where his horn is broken off just adds more to it.
Nightmare Fuel: Kyurem. As if his actual appearance wasn't enough, he has a habit of using an extremely predatory Slow Walk when stalking his targets that makes him quite imposing.