Ass Pull: After Agito becomes a tree, he is reborn from a fruit dangling from some said tree, clothes and all. While it makes thematic sense, this ability was not hinted at.
Cliché Storm: Almost all the reviews, both good and bad, noted that the movie's main flaw was that it stormed all the tropes and Aesops made famous by Studio Ghibli and played them straight, making it look like an unoriginal mix of Nausicaš of the Valley of the Wind and Princess Mononoke. Additional flaws, like the movie's tiring pacing and lack of character development, only added to it.
Fridge Horror: Schunack talks of "wiping the slate clean" in regards to humanity and keeps a firm hold on Toola even after she has served her purpose with the Ragan. It is frightful to consider what he planned to do to her after he killed all the other humans. Was he planning on repopulating it?
Moral Event Horizon: At first, Shunack may appear to be a Well-Intentioned Extremist and some people could sympathize (or even agree) with his ideal of bringing back the old civilization and his desire to undo his mistakes, even though it means destroying the Forest. Then he reveals that he intends to use E.S.T.O.C. to destroy Neutral City as well, simply out of spite. That decision shows that he has jumped off the slippery slope, no matter how much well-intentioned he used to be.
Narm: The walking volcano, in all its glorious implausibility.
Uncanny Valley: The twin forest spirits intentionally fall into this. They are basically Fair Folk, after all. Their attempts at mimicking human appearance and behavior is going to be spotty.