I think she's mad about the masturbation joke / comment. I don't think he was trying to be mean, but he was incredulous she wouldn't know that. Plus, he's nervous about the situation bc a girl he barely knows wants to see/touch his boner out of simple curiosity, and was probably trying to joke a little to ease the tension. He was just hiding behind an anatomical model with a dildo suction cupped onto it for pete's sake, then watched the girl use it as a bag holder. If he hadn't put it in his lunchbox, he would've been "the guy who got suspended for bringing a dildo to school." He's taking some major risks for her.
And it's totally realistic that she'd freak out for one reason or another. She's probably never been allowed to watch a PG-13 movie in her life.