One transgender character talks about having parents who weren't very accepting of her, but we never see them in-game and its not explained in any disturbing level of detail.
Some people misinterpreted an early cutscene as containing this. However, the character in question simply refers to the main characters by their last names and makes fun of them for trying to become adventurers, and is never shown to be transphobic despite being an unlikable character otherwise.
In-universe fictional gun violence. A town where everyone dresses up as cowboys have regular non-lethal showdowns for fun between two characters, shown once when entering the town. Some enemies also use cartoony ray guns in a dungeon.
One character passes out from getting too much magic powers and not being able to handle it, but it's not meant as a drug overdose metaphor and she recovers quickly
Main character have a mirror image of herself come to life, but it is treated like a magic possession representing her own self-doubts rather than being a head mate or alternate personality
One enemy type is a mole driving a small car, and attacks by ramming the party. This is not shown in any detail, however, and is mostly played for laughs
Minor example, you see a shadow creature look at the main character Melody during the tutorial, and you later encounter it in a dungeon where it shows up by following you
A few drug jokes (the bestiary entry for stone crabs have a character make a joke about "getting stoned") and some characters smoke cigarettes, otherwise clean
An early enemy comes in the form of a snake that bites its own tail to create a mini ouroboros, and another one is just a snake wearing a silly outfit. Late in the game there is an anthropomorphic snake character selling spellbooks in a town
Some enemies take the form of forest critters, but they're implied to be knocked out rather than killed when beating them, and nothing graphic is shown
Bees in an animal sanctuary, an enemy that's a giant snail, and robot enemies looking like beetles in one dungeon. Also some chibi crabs as enemies if that counts
One character is assumed kidnapped, before showing up unharmed. A sidequest involves the boss of a dungeon kidnapping some of your friends and having to rescue them by beating the boss
The main character Melody suffers from anxiety and gets an anxiety attack after being confronted by a mysterious entity that embodies all the things she dislikes about herself, toying with her emotions. This happens again later as well.