Initially, her and Twilight's laughing disregard for the abuse Twilight is putting her through is creepy enough on it's own merits. So much so that Rainbow and Fluttershy frequently recoil at the damage Ascentia has sustained. During the first half of the story, there aren't a lot of scenes with Ascentia in them that don't have her under some sort of serious injury.
After Twilight goes into therapy, Ascentia starts to show signs of the psychological damage that Twilight has done to her. Her mood constantly shifts, she desperately seeks Twilight's approval, and waits on her like a puppy. Firebrand explicitly states in the epilogue that Twilight had broken her completely.
Ascentia's outright obsession with Twilight is displayed numerous times. From hitting rock bottom after they broke up during high school (binge eating, getting drunk, getting tattoos of Twilight, and letting her personal hygiene deteriorate) to outright threatening Rainbow with violence when she calls Twilight crazy.
It is clear by the start of Act 2 that Ascentia is mentally unstable and suffering from Post Traumatic Stress Disorder.
Ascentia ran Twilight Velvet off the road and shot her execution-style after Velvet raped Twilight. She then killed twenty other people who had attempted to hurt Twilight in a home invasion.
When Twilight insisted on leaving for the final time, Ascentia flat out told her that Twilight would have to kill her to do it, and that she couldn't bear the thought of losing her.
Nintendogal has admitted to being terrified of Stockholm's incarnation of Ascentia.
One reader noted that the portrayal of Rainbow's struggle with her fetish for young girls was creepily accurate of actual Ephebophilia.
Sweetie Belle outright refusing to listen when she comes on to Rainbow, trying to seduce her. It's more the implications than the scene itself, given that she's a young teenager embracing her sexuality-in the wrong way. Rainbow, being an unstable woman with Ephebophilia, is put in an incredibly awkward position.
Sometimes the characters have voices in their heads, most especially when it's the one described as "Sulky" or "The Entity". Fluttershy at one point has an emotional breakdown, while Rainbow has some freakout moments of her own. We later figure out why they have these voices, but it still doesn't make them any less unnerving.
Side stories or alternate tracks to Stockholm show that Twilight abusing Ascentia never actually stops. Twilight's abuse continues. Sometimes in blatantly obvious ways, and other times in very subtle ways.
Lily has admitted that oftentimes the abusive things Twilight does is so subtle that not even Nintendogal notices it, and often mistakes it for something cute or heartwarming. Sadly Truth in Television with many cases of domestic abuse.
The Dash Family
Twilight Velvet's initial hostility toward Twilight and Ascentia comes up to eleven when it's discovered that she's been molesting Twilight since she was very little. Ascentia is aware of this early on, and outs Velvet as a pedophile after she makes too many digs at Spectrum.
Velvet goes so far as to rape Twilight in her hospital room shortly afterward.
Ascentia's diminishing mental health comes to a head in this story.
She nearly attacks Rainbow Dash when confronted about Twilight, only for Rainbow to defuse the situation.
She murders Twilight Velvet after Velvet rapes Twilight in her hospital room and seemingly has zero qualms about taking a life.
She also murders half the mob who attacks the Dash house after news of Rainbow's history gets out.
When Twilight starts making assertions that she should leave, Ascentia calls her bluff by telling her the only way she's doing that is if Twilight kills her first. These are the first inklings of a violent attachment to Twilight that goes beyond Post Traumatic Stress Disorder or a protective instinct.
The Razzle Dazzle
The only person in existence that denies Adagio seducing Sonata at fifteen being disturbing is Sonata. Even the authors admit that it's disturbing, and it remains a primary focal point for the first third of the story.
Adagio's infertility is not simple inability to conceive, it's a 98% chance of stillbirth. Who pissed in Jerry's cornflakes that morning?
The Littlest Dazzle
It's somewhat distressing to see just how easy it is for a Principal to start an illicit relationship with their student.
The scene where Maud and Pinkie witness a nuke being dropped on Karadun is surprisingly chilling.
Illicit Disco does a lot more direct interaction with the war in Karadun and in many cases the reader is given clear accounts of what goes on in that country.
Hearing Cheese Sandwich tell Pinkie about how Anevay Kortai was killed with a rock right after her birth. Jerry, who has always been squeamish, was actually sick while writing it.