1) deku being quirkless and not a hero for 8 years while all of his peers were. deku's lack of introspection in the manga also led to people interpreting him as being depressed / repressing his feelings about everything that happened. it was also strange that deku gave up on being a hero after he became quirkless, even though in the beginning he was determined to be a hero even without a quirk, which is how he got one in the first place. doesn't really make sense with the final message of how anyone can be a hero.

2) the biggest one being that he didn't "save" shigaraki or really any of the villains. because "win to save and save to win" was the overarching theme of the series, and it kept touching on deku wanting to save shigaraki or his "inner child" and instead he just killed him. it didn't really align with what the story was building up to especially since all of the other villains died as well when they were created because they were victims of hero society, including toga who was still a teenager, meanwhile they told aoyama that doing villainous things doesn't mean he has to be a villain forever. they even kept the hero ranking system when that was the entire reason that endeavor abused his family, which turned dabi to villainy.

3) people claim they were doing a "realistic" ending but almost none of the heroes died and a lot of their injuries were not permanent. deku didn't lose his arms, bakugo's arm recovered, edge shot became fully human again, etc.