Apologies if someone has covered this, or if this is the improper forum for bug reports. I didn't see mention of it in the new patch notes, or other threads on a cursory glance.
When loading a multiplayer game (Huge-Multi Random) with one other human player and multiple AIs, we discovered our supply was fairly deeply negative (-434 or so in my case). I was playing the Vasari, and had fully researched the tech to upgrade supply limits (phase communication or some such, off memory). I believe this tech was not applying, as the final stage of fleet logistics yielded 2000 supply, which was the grand total allocated. I am sure I had ~150 or so supply -surplus- when we saved and quit.
Just FYI, if further info is needed I can try to provide and/or duplicate it.