The world of Fillmore! is full of culprits and other less-than-upstanding characters whose actions are empathetically portrayed as wrong but, at the end of the day, they are kids who (usually) aren't bad at heart, break the rules for what they consider to be good reasons, and may face heartbreaking consequences from their peers or the school authorities when they're caught.
- Randall Julian in "To Mar a Stall". Once a beloved and talented macaroni collage artist, Julian started placing lower and lower in art competitions, and in a desperate bid for attention, took up tagging. Under the name Flava Sava, he tagged nearly every bathroom in X Middle School, but Fillmore caught him before he could tag the teacher's lounge. After escaping from permanent detention, Julian tries to finish what he started, only for Fillmore to catch him again and talk him down, revealing him to be a sad, lonely kid who only wants his art and hard work to be appreciated again.
- Harrison in "Cry, the Beloved Mascot". All he's ever wanted to be is a serious reporter, but he's stuck following and reporting on alleged psychic Alistair Greystone, which he considered beneath him. He framed Vern Natoma out of a last-ditch effort to finally fulfill his dream, culminating in his begging Fillmore and Ingrid to let his mascot-napping slide.
- Malika in "Red Robins Don't Fly". Originally a member of the safety patrol and Vallejo's partner, Malika was very much like Ingrid - smart, savvy, and a little odd. She went undercover to infiltrate and bust the Red Robins but was drawn in by finally feeling a sense of community with them, eventually quitting the force and becoming their leader. She clearly sees way too much of herself in Ingrid when the latter tries infiltrating the Robins again and is visibly betrayed when Ingrid reveals herself to be a plant.
- Oscar in "Next Stop Armageddon". His entire motive for wrecking all the model trains was to save his family's model train store by bringing in new customers to prevent the family from moving, only for the success of his plan gets him ostracized by his friends. Anyone who's ever had to give up a life and friends because of something similar would be able to relate.
- Biana in "Nappers Never Sleep". Lorraine was her best friend, and although she initially tries to play off Lorraine giving all her extracurriculars up as "pathetic", she was actually very hurt by it. She steals Duappy from Lorraine, hoping to drive her and Everett apart, and Lorraine back to her.
- George and his gang in "A Cold Day At X". Most of the members have something to lose if they fail the test (video game privileges, ski trips, and team eligibility), while George feels that he deserves a good grade after all the hard work he's put in. They all clearly struggle with Mrs. Cornwall's class and are under a lot of stress because of it.
- Leo/Gustav Amadeus Douglas, the sole adult culprit of the show, in "Masterstroke of Malevolence". He vandalized his own painting by drawing a mustache on it, because that was what he originally meant for it to have. He only agreed to sell it so his work could be appreciated for once. This being his only real success, he would later disappear take up a new identity as a security guard at the museum to shamefully remind himself of how he became known for what he considered to be an unfinished painting. Having taken his job seriously for 30 years before being forced into retirement, he thought it was his last chance to show his original vision before he had to leave.
- All the metal shop kids in "Two Wheels, Full Throttle, No Breaks". Their reason for stealing the scooters is so they can afford a hip replacement for the metal shop teacher's dog as a token of appreciation for what he's done for them. The only reason they fall under 'Jerkass' is because they were stealing and admit at the end how they realized there could have been other ways they could have gotten the money.
- Francine, the culprit in "The Shreds Fell Like Snowflakes" is being driven by a desire to give her depressed Broken Ace brother Frank back the job that he was traumatized by losing and get revenge on Vallejo for selfishly refusing to help Frank. Unlawfully detaining Vallejo in a very cold location costs her a lot of sympathy, but she isn't planning to detain him there for long, only endangers Fillmore and Ingrid by accident, and has also gone to a lot of trouble to create a fake crime spree rather than really destroy anyone's prized possessions. Consequently, it can feel sad that her garden of ice sculptures is mostly destroyed in the climax and Frank exposes her in spite of her actions on his behalf.
- Kipp in "Foes Don't Forgive". Cripplingly shy, Kipp has almost no friends, outsider of Dewey, his dummy, and his dog's recent litter of puppies. But when Dewey starts talking about possibly taking one of the puppies for himself, Kipp can't handle the thought of losing one of his only companions, and decides to steal Dewey's robot dog, Barcode, to make Dewey's mother believe he's not responsible enough for a dog.
- Oskar Mabini and Robert Chestnut in "Links in a Chain of Honor". Oskar just wanted to give his beloved younger sister a better future hence why he agreed to take the blame for the Lobstee claws theft and spoiler: Robert couldn't take the pressure of having to live up to the Chestnut family legacy nor the potential ramifications of having it come out that he ruined the Lobstee claws by mangling the intended message; particularly heartwrenching is how he reacts to the idea of potentially damaging his beloved sunflowers, which he can't bring himself to do and collapses to be arrested.
- Terri in "The Unseen Reflection" is a subversion in that she's simply a straight-up Woobie whose seemingly malicious acts turned out to be her (eventually successful) efforts to save her and Tori from being associated with a book series that had just horribly jumped the shark.
- Yumi and Gladys/Alexis in "Codename: Electric Haircut". Both began working on Electric Haircut because they resented the "haves" (popular kids) of X for looking down on, bullying, or outright ignoring them. Gladys, scared of the ramifications if they were caught and how the virus was corrupting Yumi, pretended to move away and changed her entire identity to hide, but Yumi found her out and blackmailed her into helping her finish the virus.
- Arthur Stanley in "Play On, Maestro, Play On", who suffers from video game addiction.
- The vigilante perpetrators in "A Dark Score Evened" - all of them have genuinely been shafted by the system, and feel they have no other option but to take matters into their own hands.
- Alexandria in "Field Trip of the Just", especially since she ends up getting a huge case of Disproportionate Retribution for her crime of poisoning a spider (which, granted, is Serious Business in this show, with Fillmore amusingly even using that exact term) despite deeply regretting the crime.
