Mine was when I was landing a rather large crew module at my successful Minmus base. Everything was going smoothly when I thought, "Hey the base lights aren't on!" So I switched vessels mid-landing to turn them on. That's when everything went to krap. I attempted to switch vessels back to the ship, but because of the games "No switching to a vessel that is crashing" protocol, I couldn't. The awful thing was that it was on a direct collision course with the base. I managed to get Velhmy out just in time to watch the module and the base get destroyed all at once. So Vehlmey was stuck on Minmus. She stayed in an old module that was launched pre-1.0 and a rescue mission was sent, which also failed. So now I have 3 Kerbals sitting on Minmus, waiting to be rescued to this day. Out of fear of another failure, I haven't sent another mission for them.
Thank God that hasn't happened to me! But why didn't you mess with the config file for it to undock?