I attacked an enemy planet with two control group fleets, numbered 1 and 2. The battle went well, and I now have both my fleets around the planet. Since I couldn't conquer it right away, because of culture, I planned to leave fleet 2 to defend it, while fleet 1 continues conquering. I expanded the empire tree panel for fleet 2, and noticed that it said it only had a Sova Carrier and two flak frigates. The pips were still there for the rest of the fleet, and hovering my mouse over it said the rest of the ships were still part of the fleet. I then went to count up the ships in the larger fleet 1, and realized that the icons in the expanded view (stacking enabled) didn't add up either. In fact, it seems as if the rest of fleet 2 is being displayed alongside fleet 1.

By pressing 1 or 2 I get the right ships selected, same with clicking on the pip groups. If I click on the stacks of ships, however, I can select ships from both fleets. None of the ships are assigned to both fleets. I haven't tried to recreate this anywhere else, but it isn't fixed by restarting the game. I'm playing with version 0.76[b].018. Sending a save file to support(at)ironcladgames(dot)com.