Are you offended that the author is making fun of certain girls (the particular girls who go to the bathroom together) or that the author is making fun of girls (a group in which a subset go to the bathroom together, and you don't want to be associated with that subset)?

Nope, still don't see it. Women tend to go to the bathroom together far more frequently than men do in my neck of the woods. It's a stereotype, but I don't see how it's a harmful one to perpetuate, unlike your example. Would it bother you if people assumed you wanted to go to the bathroom in a group? If so, is this a common concern?