Don't worry too much about it. Middle school girls change alliances all the time. The best friend this week is personna non grata next week. The groups morph and change all the time, too. Worrying about every incident will drive you crazy.
My stepdaughter had a falling out with her best friend in 5th grade (no one knows why, really) and by 6th they were inseparable again. Some friendships will be steady, some will come and go, and some will be so transient that you'll barely notice they're gone. I'd only be concerned if she talks about being bullied (or bullying others) or if other serious issues come up. Occasionally we have talked to our now 13 yr old about being a good friend and that she should be civil to people, even if she doesn't like them, but mostly we stay out of it unless she comes to us about a problem. It doesn't seem to help when we try to intervene on normal middle school girl drama. Hang in there!