I encountered this as well a few times before, the only problem that I did it in the vanila game. It is a problem with the engine itself I believe. As much as I figured it only comes out if you press the pause button at the very same microsecond a space/ground battle would commence and the engine can't handle it, since it would pause the GC for the battle anyway, and an another pause order came in. this makes it do all sorts of weirdness and sadly there is no fixing it.
You should load a save game from before the bug or start a new game.
Sorry m8.