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.
Likewise, the Evil Enchantress of Everfree Forest was built up for a few chapters, only to be unceremoniously defeated by Twillight's Deus ex Machina in the same chapter she finally appeared. Pinkie Pie even lampshades this.
Pinkie Pie: This whole Everfree Forest plot was totally pointless and Zecora should’ve gotten more screentime.
Big-Lipped Alligator Moment: The new lead guard takes an arrow to the knee before he can shoot Twillight. The event is never mentioned again, despite being completely out of place in the story's general world where guns are the weapon of choice.
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.
Romantic Plot Tumor: Rarity, Applejack, and Pinkie Pie all abruptly declare themselves lesbians for what seems to be dramatic tension. After a few paragraphs, their relationships never come up again.
Strangled by the Red String: Applejack and Rarity, who admit that they've fallen in love with each other the moment Admiral Awesome says that they're in love.
And Rainbow Dash's love for Pinkie Pie, which was similarly spontaneous.
