A dragon landed (as usual) on the College's courtyard. Arniel, of all people, started launching ice storms at it and a couple of them must've caught Lydia, also fighting it on the ground. Once the dragon was dead, she went all out on him, with a college guard (part of Cutting Room Floor) going after her.
Anyway, I froze the game with tfc 1 to resetai & stopcombat on all of them. When all was said and done, Lydia was like "Well, this is a nice mess you've gotten me into" and the "Let's go. Let me worry about the guards" option showed up in the dialogue list. The moment I got her bounty on me, the guard went hostile and before I could do anything, she charged in and two-shot him. Blame the gear I've given her...
Reloaded and killed the dragon again -this time, without the friendly fire incident. Still, I had no idea followers can get bounty...