In the optional area The Beehive, a character refers to their group as "my queers", and another character expresses homophobic sentiments towards them.
You are forced to make many difficult choices throughout your journey, a few of which can result in amputation. It's not uncommon for a player to reach the end of the game with the protagonist missing one or even both arms.
It's the central plot of the game. Also, your party members can be kidnapped when you heal, and a different character is kidnapped for sexual purposes in the first act of the game.
A truck specifically, in the first act. The scene cuts to black before the collision with an appropriate sound effect. There is also a party member who can attack with a "Truck Slam", though it's not at all graphic.