Just wanted to throw in my few cents here, I've had the same bug with some fleets.
It happened to me once when playing space marines. After leaving a skirmish battle very early on or even during deployment phase, this bug showed up later on in all ranked games on all ships from the start (that is - two games, I've restarted the game after that).
Another happened to me a few times playing
aeldari eldar, it seems to happen sometimes when you are too fast or aggresive about pressing repair button. It also seems that eldar retain their ability to use vaul's manuever (or whatever it's called now)