Fiona into thinking Prince Charming is Shrek. Shrek is also gaslighted into thinking Fiona is better off without him. Both instances are done by the Fairy godmother.
Fiona is locked in a tower as a child because of her curse and a cure for the curse is arranged without her knowledge by having her married off as an adult.
While there is no sexual assault, a character does impersonate Shrek and make advances on Fiona that clearly make her uncomfortable to try and make her fall in love with him.
There’s a short scene in the end where the “ugly stepsister” goes to kiss Prince Charming, and you can tell he is visibly uncomfortable with this. It’s shown as if this is his punishment for being an antagonist in the movie.
Two anthropomorphic trees arm wrestle, causing one of their arms to break off.
When the giant gingerbread man is attempting to storm the castle, his arms break off.
The Big Bad Wolf, who wears a dress, is called "gender confused" by the Fairy Godmother. Doris, who is a woman but happens to have some traditionally "masculine" traits like deep voice, facial features and body build, is treated as ugly and not fully passing.
Fairy godmother refers to the wolf as "gender confused", the ugly sister is implied to be a trans woman who doesn't "pass" and pinocchio is mocked for wearing ladies underwear