I found an interesting bug... While playing as the borg, I had a fleet (8 ships) of interceptors and used their special ability to transwarp across the map. The ships transwarped away like normal and never emerged on the other side. They disappeared! I tried again with another full fleet and the same thing happened. I tried again with one ship and it worked normally. The special ability works up to 6 ships. Any more and they'll disappear.

Also, near the end of the skirmish, I set a full group of cubes to search and destroy, and.... poof! gone. Setting the ships individually works fine.