Karyn could have been smart about this and just wish to know why her most recent wish had changed her into a boy, but no, that's not what happened. She was so weirded out by her change from female to male that she instead said "I wish I was a girl."
But when nothing happened, it made her even more worried. Why couldn't she be female again? She never wished to be a boy, so how come this wasn't working?
Well, the reason it wasn't working was because she was Karl, Jon's crush. Jon was gay now, so his crush would have to be male. If Karl was Karyn again, then she wouldn't be male, thus causing a clear contradiction. Maybe the stone could have come up with some kind of result to work around the problem, but it "chose" to keep things simple and not grant the wish at all.
Karyn/Karl was panicking a bit now. Was she/he stuck like this now? As a boy who had a secret crossdressing fetish? Was there no way back?