Not sure about that specific bug, for the moment I'll let Keith chase that one if there's a save or similar. But, I thought I'd pop by to mention: wave caps are going bye-bye in the near future. The only reason for having the caps was to prevent the extreme wave sizes from turning the game into a slideshow -- or worse -- but there are other ways of doing that now, thankfully. Excess ships above the wave cap of 2000 will just appear inside carriers, so that they don't all come out at once unless someone is foolish enough to attack the carriers before killing the existing AI ships.
Just figured I would throw that out there, because with the current wave caps it's pretty hard for the waves to have much in the way of teeth, especially at the higher AIP levels. This should make it so that exponential AIP gain doesn't cap out the actual danger of the AI in the way that it always had, so that eventually it gets so ridiculous it crushes you no matter what. Right now there are some people surviving at 4000+ AI Progress, which is okay I guess, but the caps are making it easier than it should have been. And it's hobbling difficulty 10, too.