Ive never noticed this problem in regular EoW and thought it would be fixed, but now I am experiencing the same problem with FoC. Ive only had this problem so far with Tyber and Urai, but sometimes when they get killed , the respawn timer does not start up so they never respawn. The hero icon shows up as though they should be alive, but they never reappear. I couldnt really say what triggers that to happen because I really dont know. Sometimes its auto-resolve, one time he got killed just as he was about to retreat so during the retreat "cutscene" his ship was exploding.
There was also a bug that occured when I was attacked by the rebels, where they won, and when I sent a fleet to retake the system, the icon for the rebel fleet showed up, but a battle never initiated. I then sent my fleet to a few other systems, and battles would never initiate despite the fact that fleets were present as shown by the rebel & imperial fleet icons on the map.
Ive had no problems with skirmish so thats all good, at least to my knowledge.
Hopefully this will be addressed in the first patch, because these bugs seriously effect the ability to play the game. No the game is not modded, and yes its a fresh install of EoW and FoC. This is a pure gameplay issue.
Both of these problems only happened once each in seperate games of GC.