Ok, I had to open my big fat mouth. Right after I posted that I had the Altarians surrender to me and the game completely flipped out. I now have a few ships with 0 move, 0/0 hp, no thumbnails, and I seem to have gone to 0 logistics. Additionally, all my racial abilities went to zero so all my planets are unhappy and more than a few are losing money.
Not a bug. You just got hit by the disease mega event. Reduces all your abilities to zero-your planets are unhappy because your morale's zero, and you're losing money because you can't afford to tax them that high anymore, as well as not having your economic bonuses anymore, either.
Research disease cure in the tech tree (doesn't show up until the event happens, and even then in TA you need to go delve into the structure of the tree under xeno biology to find it) and it'll fix most, if not all, of your problems. Someone reported not having fleets still after curing the disease, but I think that was a fluke.
Additionally, I'm not 100% sure it's disease, it may be plague, as I always get those two confused, but the same advice applies and in any case you should only be seeing one of them available in your tech tree anyway.