To clarify: The game stars a group of unbelievably monstrous girls (The aforementioned "Red Crayon Aristocrats") who torment the main character, forcing her to do their bidding and then rebuke her efforts every time. Then, the one girl who was nice to you turns out to be the one behind it all along. Do note however, that from the perspective this is all told from, some of the girls' attitudes and behaviors may be a result of Unreliable Narrator.
Overlord II opens up with the son of the previous Overlord as a child being pelted with snowballs by some kids in his village. This is of course a case of Bullying a Dragon when the "Witch-Boy" returns to fulfill his duties as an Evil Overlord.
Inazuma Eleven 3: Sekai e no Chousen: Bomber starts by showing The Rival Rococo being bullied by bigger, stronger kids in his childhood.
Villains in Inazuma Eleven series tend to be on an extreme end when it comes to fantasy violence. Sure, it's limited to soccer, but they are still egotismic children who enjoy invoking total humiliation, destroying propoties, and playing unfair - with little to no remorse until their destined Heel–Face Turn.
Iris, from RosenkreuzStilette. She disguises herself as an innocent girl to hide that from everybody.
In Katawa Shoujo, Hanako, whose body was severely scarred in a house fire that killed both her parents, was bullied by her classmates for her appearance when she returned to school, including several of her former friends.
The Skull Kid in The Legend of Zelda: Majora's Mask. The carnage that he invokes is fundamentally caused by his innocent inability to understand adult relationships and responsibilities, and a childlike egocentricity that makes him regard inattention toward himself as a deliberate insult. Thanks to Sanity Slippage from the Mask, he decides the appropriate response is to curse everyone he meets and set up the destruction of the world.
The Bombers can occasionally fit this as well. While their job is helping out others in town, Jim is plenty rude if Link talks to him while he's playing games. The other kids all refuse to let Deku Link officially join their club because he's not human. Granted this mindset was implied to to have sprung from their last non-human member (the Skullkid) causing trouble instead of helping others, thus making them reluctant to take another chance, but still.
Pretty much the entire school goes feral in Our Darker Purpose when all the teachers disappear. Most notable are Regan and Goneril, who arrange an outright massacre of weak, quiet students.
In The Dead Case, there is a group of children who torment a little girl repeatedly. The first time the protagonist comes across them, he must scare them away. Later, the school ghost scares them away and protects the girl.
Mangle (or presumably, Toy Foxy) from Five Nights at Freddy's 2 was an animatronic specifically made to be more kid-friendly and cheerful than the original version, and to entertain them. They immediately, brutally tore her apart, so many times that the staff eventually gave up trying to fix her and left her as a heap of, well, mangled parts.
Since the main protagonist is a child in Undertale, you can invoke the trope by having said child slaughter every single monster with some of them being actively afraid of you when you show up after you amassed a high body count. The trope also applies to the first Fallen Child, who wanted to kill everyone in their village by committing suicide, so that their soul could merge with their best friend's soul, creating an immensely powerful being the Fallen Child could use to slaughter all the humans.