These are some bugs I discovered in my most recent 14 hour game:
Multiple capital ships target the same object with the same special ability at the same time. For instance, 2 or 3 Dunovs use shield restore on the same Kol, or they use the Magnetize ability on the same enemy target.
When you click to place a structure in the gravity well at the same time that autosave kicks in, the structure places at the point of your mouse cursor when the autosave finishes instead of where you clicked.
After killing all the enemies in the game, the game continues to run in the background (and autosave) while looking through the graphs.
The ship counting on the end-of-game stats is messed up. The Arn had -23 frigates, Trade Coalition had -1, and Toandum Faction had -2. My guess is that you are counting some ship as a frigate that should not be a frigate (like maybe the LEV Constructors)? The other ships all correctly balanced to 0.
Lots of fighters/bombers + special ability usage = NVidia driver crash in nvlddmkm under Windows Vista 64-bit (dxdiag64 output E-mailed to support with link to this thread). Fortunately, Vista recovers and restarts the drivers and the game keeps going (just pauses for a brief moment while it restarts the drivers).