Right after Indika runs over the last wood board in the windmill, grabbing Ilja's hand.
You hear a squal and the game then shows an unneccessarily long closeup of the dog/wolf's head hanging between some gears. Really upsetting.
Note below the dog topic
Also after Indika opens the letter, we see a giant cow getting split in half whenever her mind runs dark. While this szenario seems to only be Indika's imaginagion it still could be mildly disturbing.
Idk if this counts really since we don't see THAT much nor do we see it happen but there's a guy impaled by metal bars.
Otherwise maybe check the notes below the animal topics
The player interrupts before anything specific happens (read below the sexual assault point for more info)
Edit:
Towards the end, when Indika is in thw prison cell, it is heavily implied that she got forced to do something. Again we do not see it thought.
Yes, Indika cuts Ilja's arm off to save him. You see it very much coming so there's plenty time to look away, although we don't see the actual process. It's a very tense situation though.
First when Indika arrives at tge crashed train a doctor gives a dying man morphine.
Later, when Indika checks on Ilja's arm, she gives him probably morphine as well
You hear a squal and the game then shows an unneccessarily long closeup of the dog/wolf's head hanging between some gears. Really upsetting.