It could be that Percy was being overly flirty with another girl in the fanfiction. Annabeth is proud and has feelings for Percy, so seeing him act that way might make her angry enough to slap him. It's a way to show her jealousy and her sense of possession over Percy in the context of their relationship.
Well, one possible reason could be that Percy made a really stupid decision without consulting Annabeth first. Like, if he went off on a dangerous mission on his own when they were supposed to be a team. Annabeth is a very strategic person and she might feel betrayed or extremely frustrated by such actions.