Angst? What Angst?: Twillight's reaction to learning that Celesia is evil definitely qualifies.
Anti-Climax Boss: The Tyrant is one in-universe—despite being played up as a major threat for over half the story, he dies extremely quickly in an explosion. Twillight wasn't even trying to fight him—he just gets caught and dies.
There's also Twillight abruptly discovering every villain from the show—including ones who aren't featured anywhere else in the story, such as Discord or the Smooze—right before fighting Celesia. She wipes them out in one sentence, and they're never brought up again.