She may be feeling very bad and insecure and she needs reassurance and doesn't know how to get it. She may be starting fights when what she really needs is your time and attention and reassurance. The changing hormones may have her questioning her body and whether she will be attractive to you.
You should spend time with her and hold her and let her know she is important to you and nothing will change it. Be strong and don't get your feelings hurt if she says ugly things. Be the calm and strong one. You may object to her words and say you are sorry she has been going through a lot and you have been away at a bad time, but she doesn't have permission to be verbally abusive. And then hold her and love her.
It may have always been an issue that she let slide by because she felt she couldn't talk about it or any number of other reasons. The hormones and the distance might just be helping her have a voice. The distance probably has her missing you, and depending how she deals with emotions such as missing someone, she may be looking for something to overshadow the sad emotion.
I'd definitely talk through the issues as dismissing them is going to make you look bad. So will saying, "I thought we already dealt with that!" because, to her, it may be "obvious" that you really haven't and comes across as either ignorant or dismissive. So long as you handle this with care and consideration for her feelings, I don't foresee any problems being added to those in the past.