I'm not sure how related it is, but I had a weird thing happen in Winterhold with Lydia. When the magic nodes things were invading the town, when the fight was over, Lydia had become a follower of on the College mages. When I went to swap inventory with her after the fight ended, it listed her as "So and so's Lydia" much like when they conjure something and it says "So and so's flame atronach" and I could not start dialog with her. Not sure what was gong on, I fast traveled away and came back only to find a pile of ash in the town street that held all the inventory I had given Lydia. I ended up reverting to an earlier save.
Mmmh.. this is not a bug.. She was more than likely killed, and resurrected by a fellow wizard..
not tried to have anyone else follow me, and have no saves before i had her wait for me in my room at the college...going to carry on and see if she re appears at my home in Whiterun...not impressed that this has happened, if its just the game code forgetting to load her in the location she was told to wait so now she has gone for good Bethesda will look more crap in my eyes then they already do
How long did you wait..? (in game time) +/- 72 hours should dismiss her..
Edit: there are also quests which forcefully remove your current follower.. (companions for one..)