Nightmare Fuel / Old Mare Luna

• When Luna and Discord made their way to Griffonstone, they noticed it was littered with charred griffon corpses as a result of an attack the lava demons did.
• King Sombra brutally murdering Cadence and Shining Armor. Especially Shining Armor because he stabbed so many crystals through him, he managed to stab one of his eyes out. Even Discord was disturbed by this.
• Grogar bringing Fluttershy's corpse to Discord. Along with it triggering a Heroic BSoD in Discord, the state of the corpse itself was not pleasant. Her flesh and wings have been burnt, her eyes were now gone and there were only a few strands of her hair left. It's even worse when you realize Luna did that to her.
• Cozy Glow has not improved with age. Along with retaining her Faux Affably Evil demeanor, she also threatens to put ponies to sleep if they do not follow her idea of friendship. It's even worse when the Dazzlings encounter her in person, where's she's a shrivelled barely alive husk attached to some magical crystals keeping her alive.
• King Sombra tricking Luna into killing the Mane Six, Celestia and Star-Swirl. Not only that but the sheer brutality Luna inflicted upon them, thinking they were the villains.
• Discord grabbing Luna by the throat and snarling at her after she told him about what happened on the day King Sombra took over Equestria. Since Discord has been relatively happy up until this point, moments where he had mourned for Fluttershy notwithstanding, to see him so angry at Luna after all they've been through in the story is a bit scary to witness.

  Discord: You killed Fluttershy?

• The ponies in Chrysalis' territory. They have been rendered emotionless by Chrysalis feeding off of their love for bloodshed. And what's worse is that most of them are from other territories that came to her territory willingly because it was better than living in the territories of Grogar, Cozy Glow and Tirek.
• When Sunburst managed to break Starlight free from Sombra's control, Sombra stabs Sunburst through the stomach and forces him to watch as he painfully took over Starlight's mind again. There is also what Starlight says once Sombra has taken control of her again, which is even more haunting since they were the last words Sunburst would ever hear her say.

  Starlight: Just give up.

• As much as she deserved it, Discord's brutal No-Holds-Barred Beatdown on Cosmos. Even Discord was horrified by what he did since he never killed anyone before.