Thanks thammer for making me think it through. You are correct, the mags would be hot by virtue of the mag switch being accidently left ON, regardless of whether there was still power on the bus. So the issue becomes, an extra battery on the electronics side of the switch would potentially energize an intercom, radio, beacon, interior lamp, or other device normally turned OFF by the master, until the voltage dropped enough to possibly damage the electronics.
As for an unreliable connection:
I've had something similar happen on motorcycles due to the 12v receptical's ground failing. Usually, some fine steel wool swished around inside the receptical (make sure it's not hot unless you like fireworks, or you can use fine sandpaper) will clean off the invisible crud/film that builds up over time. In one case, the ground wire connection on the receptical needed to be removed, cleaned, and reinstalled.
** Edited to confirm my faulty logic. Thanks, thammer **