I encountered this bug too by going out of physics range via an EVA on Minmus and then coming back.
Workaround to save your game again: destroy the Vessel. Probably just the buggy command pod would be enough.
I did a rendezvous with my spacestation in LKO before the end of a mission, EVA the kerbals and science to the station and then let the mission-craft disintegrate in the atmosphere.
As soon as the buggy pod was destroyed I was able to save the game again.