This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Mad Father
You'll find various corpses in random places throughout your journey. It's even disturbing when Aya comes across corpses of kids her age, maybe even younger.
Some of the souls you need to help to get gems classify.
Aya's father as a whole. ESPECIALLY when he chases down Aya to kill her and make her a doll.
That laugh and his screams. It was frightening the moment you feel trapped in some areas.
The adjacent room to the one with the stuffed dog. One of the gems requires you to give the stuffed dog a bone, but you can't do that unless you get one later and then backtrack, and there's no other reason to come back. When you go back into the stuffed dog room, the other room has half of a bloated doll sticking up out of the floor in a pool of blood, which is bad enough. But if you leave the stuffed dog room and come back in, the bloated doll will be fully out of the floor and facing the wall that separates the two rooms. There's no reason to go back into either of those rooms once you've done the dog puzzle; Developers' Foresight, it seems.
In the new Steam version, the bloated doll has been removed, and replaced by a ragdoll hanging from the ceiling in a hangman's noose. Unlike the bloated doll, she only appears the first time you enter - after exiting and reentering, she's gone.
The little boy in the kitchen tells Aya that the ham tastes just like Mom.
It Makes Sense In Context: That was a literal translation. The context itself translates better as saying it "tastes just like how Mom makes it." This has been corrected in more recent updates.
The mad father's creations, especially for people who find dolls creepy in the first place!
The first soul you see in the room next to Aya's, and the nice Jump Scare she delivers. GIVE! GIVE HER BACK! MY DAUGHTER!
Aya witnessing her father stabbing her mother in the chest.
The fact that Aya turns out to be just like her father.
One word: ""AAAAAAaaaaaayaaaaaaaa......" And it's voiced, too!
In the Steam version, the scene in the trick room has been completely changed - it used to show a king watching two knights duel; now it depicts a dead girl lying on an altar surrounded by nuns and priests. Once you complete the puzzle, making the right side of the room match the left, the dead girl over on the left side will suddenly sit up in the middle of her funeral... but if you go back to the left side to investigate, you'll find her lying down again.