Specifically, are the scenes with the leches, trepannation, etc. flashbacks or hallucinations. I recently wrote a fan fiction which discusses the incidents as though they actually happened in-universe, and I got flamed terribly for it. Did I mess something up or are people on the internet just generally terrible?
The "asylum section" is like a backstory of what happened to Alice in her stay at Rutledge. It really did happen to her. Your fanfic may have just offended readers. Maybe they can't tolerate the horrible things Alice gone through. Or they didn't completely understand or grasp the events of the storyline of the game.