The moment there was even a suggestion he hadn't done it, I pegged her for it, since she was really the only other person in the story who could have without it being some random Classmate C we hadn't been introduced to yet.
Given how messed up this bully guy is, I can only imagine what he did to her to promp this girl to cast Exodia's obliterate on his face. Probably something to do with that guy she's supposedly going out with despite seemingly interested in the protagonist.