The citizens of Wellington Wells are gaslit about their tragic history, both by their government and each other, and expected to either forget what happened or lie to themselves.
There are Doctor enemies that can forcefully inject you with drugs via a syringe. Very early in the game you see this happen to an npc (but you can just walk by without looking).
A character is implied to have autism and another main character does take advantage of this at one point. It's also implied that his parents may have been abusive towards him.
If you die while playing through Arthur Hastings' story mode, you receive a newspaper snippet that mentions him being a confirmed bachelor", a way to imply that he identifies as LGBT (commonly as a way to say that someone is gay). However, Arthur was involved romantically with Sally Boyle, implying that he is bisexual. As it is a player character's death, it is avoidable.
The base game has relatively happy endings; but in the dlc we all fall down, which ends the story of wellington as a whole, wellington burns to the ground and many people kill eachother in the streets