Girl's cycles can be very irregular when they're young. It's nothing to worry about. Touching herself will not affect her cycle in any way. Imagine how that would mess everyone up if that were the case.
She should think about seeing her doctor just to start having regular physicals and gynecological exams.
Don't think that you are doing anything wrong or can possibly mess anything up by being open and intimate with each other and with your own bodies. If you were having sex, that would be different. If you choose to have sex before or after marriage (your choice either way), just be safe about it and use protection if you don't want her to get pregnant. Other than that, you cannot mess up her cycle. Only pregnancy and hormones can do that.