I'have been having this issue since I play the mod and I'm surprised no one else wrote about it yet.
It usually occurs after long playtime (10-15 hours, I guess). The issue is that during a space battle once I lost control over my units. I can not click on them, I can not oder them anything. Once it occurs, I have to reload an older saved game because it totally messes the game.
I can not move units amongst planets, which is a new effect, I have not experienced that in older versions.
Also when it happens, I can not see the hardpoints of the units anymore.
I played art of war with Empire on hard. It happened against the Eoth and NR, as well.
Have you ever seen anything like that?