In Juniper's Knot the fiend says she has done many things: she has killed many people, saved children, destroyed entire towns...but none of those are the reason she is confined within the magical circle that keeps her prisoner. She never reveals why she ended up there, but only angrily dismisses the question.
In Tsukihime's side-story game, Kagetsu Tohya, Shiki occasionally refers to the haunted house his class did last year, in which he and his friend were responsible for something that resulted in their student government making an amendment that strictly prohibits tea kettle monsters, mushroom monsters, and any pot that uses the aforementioned things. The specifics are left up to the imagination.
Shiki: Yes, we did a haunted house my freshman year, too. Well, Arihiko did his part so ardently that we were forced to stop in the morning. (To himself):The Inuidake Children Kidnapping. It's an event that will forever remain in the annals of the student government.
Dangan Ronpa: Monobear scoffs at the notion of explaining how he erased the students' memories of their two years at Hope's Peak Academy.
Everything that happens at the Nevada Test Site in Virtue's Last Reward counts as one of these. Untill the sequel, that is.