Broken Base: For What's Done in the Dark..., readers are split over who is less in the wrong: Shining and Luna for literally screwing Cadance over, or Cadance for her tantrum involving maiming her old mentor, trying to have Luna banished to the moon again, and seceding from Equestria.
Complete Monster: Feather Duster, despite being mainly a flashback character, is the Big Bad of the "Dear Cutie Mark Crusaders" arc. After being fired from the Ponyville weather team for drunkenly flooding the rabbit holes during Winter Wrap-Up, he takes revenge by "testing" Rainbow Dash (his replacement as captain) with a catastrophic, unscheduled storm which results in the death of Applejack's parents, and he would have let her face the wrath of almost the entirety of Ponyville (since the captain is the only one with access to the storm-generating machines) if he hadn't passed out drunkat the scene of the crime. Later, he lashes out at her again (whether for misplaced revenge or sheer evulz is unclear, as Dash claims he always seemed to hate her even before he was fired) by attacking the orphanage where she grew up, fatally wounding her mother figure Firefly, kidnapping Scootaloo (who had just been found at said orphanage), and forcing Dash to choose between saving Scootaloo and stopping him from unleashing an even bigger storm. Dash, after pulling off both, ends up throwing him into a point-blank Sonic Rainboom just to keep him from hurting anypony else. Even that doesn't put an end to his villainy. In the followup "Cutie Mark Crusaders Dream Warriors," it is revealed his spirit was pushed into the dreamscape, allowing him to haunt the Cutie Mark Crusaders' nightmares years later and feed on their fear ala Freddy Krueger then attempt to take over Scootaloo's body to murder Rainbow Dash, before he is finally literally bucked into Tartarus.
Darkness-Induced Audience Apathy: The increasing focus on foreshadowing/setting up a coming cataclysmic conflict which portends doom for Equestria, and the distinct possibility of unhappy endings for most characters involved, has driven off a few readers (though many more are still hooked). Some also find the behavior of the royals who receive much of the focus to be extremely unpleasant, especially considering that their divisive behavior is implied to be at least partially responsible for said conflict.