There are several dog-like enemies toward the beginning of the game that can be fought, but the flavor text after battle states "The Runaway Dog became tame!" and it is implied that they do not die.
Pokey's dad is heavily implied to abuse him and his brother. The English version downplays it by cutting out references to him hitting the boys, but still leaves the implication of verbal abuse with him yelling at his kids. And the writing (Pokey and Picky are "really going to get it") and sound effects are vague enough that they could easily be mistaken for him still hitting them, especially if you don't speak to Pokey after he's punished by his dad.
Pokey/Porky is an a dysfunctional household and in the Japanese release is beat by his father for sneaking out at night. In the localization, it was heavily toned down.
Pokey and Picky have abusive parents. Pokey becomes a major villain, and his toxic frenemy relationship with Ness could be read as abusive as well (at least inasmuch as it can be given their age). Picky on the other hand is nothing but pleasant.
While undergoing spiritual training as Poo, the player is, in an illusion, required to consent to their character's legs and arms being removed and "thrown to the crows" (during which the character takes damage), then ears (after which game audio is muted), then eyes being removed (after which the screen fades to black).
The amputation is not depicted visually and the character is shown whole in subsequent scenes.
During Poo's spiritual training, the player is required to consent to the character's eyes being removed, which is visually represented by a fade to black. (This does turn out to be an illusion.)
The game is mostly bloodless, and the characters go unconscious when their health reaches zero. However, one of the characters is mutilated, albeit it is not shown, and is revealed to be in an illusion.
The player characters are children who can be defeated in battle. While the game refers to them as "unconscious" and they can be recovered at a hospital, while they are in this state they are depicted as angels (transparent, winged, with halos).
The character Paula is introduced by being kidnapped and held captive for a human sacrifice ritual (which is thwarted and not described with much seriousness).
A main character is said to be prone to wet the bed, and in dialogue it's said people will wet themselves or have wet themselves, but this is not depicted.
Monotoli laments the shape and weakness of his body after losing the power of the Mani Mani statue.
Buzz Buzz is taunted about being stuck in the body of an insect.
Brick Road does not express unhappiness with his body but carries out an ambition to have a doctor drastically change his body.
The use of certain attacks, specifically psychic (or PSI) attacks, make use of many incredibly jarring, bright, and colorful strobe lights. Even as a person without sensitivities and playing in a well-lit room on a small screen, I was bothered by it; people with epilepsy should stay away.
You, the player, are given the option to enter your name into the game. This becomes a plot point during the final boss (though not in a way that's intended to be scary).
No, but (SPOILERS) there's a disturbing (and disproven) fan theory that the final battle is Ness and his friends going back in time to abort Giygas as a fetus.
The main character, Ness, is made fun of for being fat by several characters on 2 different occasions despite his sprite not indicating that he's overweight. Pokey/Porky, a character who is overweight, is commonly referred to as "some chubby kid" by npcs who do not know his name, and there are quite a few jokes about his weight and how much he eats.
The Happy Happy Cult is based off a real life religious cult and thus shares a few elements. Furthermore, Paula is religious (likely Christian) and has pray as a command.
A strange woman in a bikini lures you and your companion into a strange hotel, which ends up being a trap. This is required to progress. One NPC says that he would "like to spend some time with her".