Not really, but we find out late in the game that Clara and Mia (the conjoined twins from the alternate reality) were actually real girls who suffered horrific medical abuse. When Fran meets them in the alternate reality, they can be quite cruel to her.
Fran and many of the other patients at the asylum are victims of severe medical abuse. One of the patients is also a victim of sexual abuse, although this is only stated, not shown.
Alchohol isn't abused. There is one occasion that I recall where an npc is drunk, but it's not abuse. The game does revolve around heavy substance abuse, but it's pills, not alchohol.
The security guard at the hospital tells Fran that he'll give her a key in exchange for a kiss. It doesn't happen. Also, two of the children in the hospital are revealed to be sexual assault victims.
Early in the game a child in the ward is shown with a looming shadow over her thrusting against her. She was sexually assaulted so bad she almost died & now suffers from mental health issues. You can also see bloody handprints over her crotch and chest.
A lot of corpses, dismemberment, and graphic injuries. There's one scene in particular where Fran is being magically transformed from a tree back into a human, and the image that shows onscreen is very disturbing.
I guess it depends on your definition of amputation. In the beginning sequence, Fran's parents are shown dead with various body parts severed from their bodies. Severed body parts appear more throughout the game.
When Fran reaches the hospital basement, Remor confronts her at the top of the steps and she faints, waking up at the bottom of the steps. She isn't injured.
Even characters who aren't really dead will often have their corpses shown in hallucinations, and several characters actually die (Fran's parents, Clara and Mia, the Beetlepig, etc)
You learn in the opening sequence that both of the main character's parents have been brutally murdered. There are depictions of their dismembered bodies.
In episode 1 after Fran falls down the vent and walks up the stairs, there are two doors on the right (the room with the horse). If you look trough the right door window there is a boy lying on the ground with puke next to his head.
In episode 2 when you meet Antonio the greatest and he tells you his beetlepig ate your cat, there's a dialogue option that says "make it vomit", it won't no matter what you option you choose
One of the children in the beginning of the game is shown with cuts on her arm, referring to the blood as 'red milk'. This was quite unsettling for me, so if this is triggering to anyone else do be careful.
In Clara and Mia's attic, you can interact with a baby carriage that is revealed to have conjoined babies in it. They stare at you for a few seconds, then start to cry with distorted sound
In the alternate reality, there is a hanging skeleton with a blood trail from an aborted fetus crawling away. There are multiple dead/mutilated fetuses in the game.
one scene that comes to mind has a skeleton of (presumably) a pregnant woman; her umbilical cord is tied around her spine and there's a lump covered by a blanket attached to it on the floor (which is obviously a baby). you have to see it to progress.
In the first chapter when fran asks the security guard for the key he says that he'll only give it to her if she gives him a kiss (she is only 10 years old btw)
Fran cannot swim so if you fail the frog mini game then it is implied that she drowns, it is not graphic though and you get to restart the mini game, you also have an option to skip the mini game