Every single scene involving the serial killer The Carver.
There's also the way Colleen Rose killed a rival talent agent. She jammed the hose for a teddy bear-stuffing machine down his throat and flicked it on, then finished her new creation by pinning two button eyes onto his. Not to mention the close-up of the victim's still-horrified, lifeless face, with those black eyes, blood tricking down his cheeks like tears. And later, when his body is found. Horrifying flashbacks of the actual murder ensue for the audience. The person who finds the body has the same reaction as the audience.
When Matt beats up the innocent trans woman Cherry Peck. This scene is particularly horrifying to LGBT people who've faced violence.
The whole scene in which Matt and Cherry were held hostage in that scary white supremacist guy's basement. Something about the way Cherry flinched in fear when she is threatened is too realistic for comfort.
The man singing as his leg had to be amputated after the plane crash.
The man who had the compulsive need to mutilate his face.
When Matt and his friend nearly killed that girl after they decided to get high and drive around.
At the beginning of season 3, when Matt found the rotten corpse of Adrian.
In one episode, the patient is conscious during her surgery, can feel all of the pain, and screams and begs for the doctors to stop in voice-over.