I've played GalCiv II v1.0x about, oh, 30-40 hours now. Besides being the most rewarding 4X space game I've ever played, here's a few bugs I noticed. Most of these I noticed in a gigantic size 9-player game. These are roughly in order of annoyance.
1. Rally point scroll browsing doesn't work. When I use the menu to send a ship/other to a rally point, I can't scroll down the list of rally points.
2. Rally points saving/deleting is not working properly. I created 3 rally points, deleted one, list was OK, then deleted the remaining 2 and created two brand new ones. After loading the game later on the rally points were no longer in the list, but the old deleted ones were. However, on the map display, everything looks as it should be, with only the two newer ones appearing.
3. Move exploit: I can get free moves by moving a ship into an already moved fleet (no more movement left), and joining it. The new fleet now has as many moves left as the one that just joined, rather than zero.
4. Saving an upgraded ship design under the same name causes problems. Both designs appear, with the same name, but only the more recent one can be built.
5. Culture domination bug: once in a small game and once in the gigantic game, one of the races (Altarian in the gigantic) suddenly has influence over every pixel of the map. No-one else's influence is left. You get some reports from some of your planets about this, but not all of them. The game doesn't end. This is remedied by saving and loading, and everything is back to normal on loading.
6. Sensor glitch: this is rare, but sometimes a fleet will "forget" what its best sensor range is, and will use the sensor range of one of the inferior ships in the fleet. This is remedied by deselecting and selecting the fleet a few times.
7. Viewing ships in a busy starport: If an opponent race has a planet that has more than one row of ships in the little starport display, selecting and deselecting them gets screwed up. Sticking to one row works fine, but once you select a ship on the second row, the previously selected ship in the first row remains selecting, and this makes it hard to examine the ships. This is remedied by deselecting and selecting the planet.
8. Offers to cooperate: I only get a suggestion by an alien race to cooperate (not ally or attack) against another race after restarting GalCiv II and loading a game. They're not offering any kind of trade, and aren't especially responsive when I offer the obvious trade. The bug is that it *only* happens after restarting GalCiv II.
9. Shortest war ever: A few time a minor race (Andians) that built small influence bases in the middle of my empire got pissed off about nearby transports and declared war. However, immediately after doing so, I can offer a straight up peace treaty and they'll accept.
10. Upgrading a ship: Removing components can sometimes be glitchy. Remove one from the end, and the component is removed from the ship, but not the compenent list. However, scroll back to the left, and the right scroll button goes dark, showing the component was removed, but the component list didn't refresh until scrolling. This doesn't always happen, selecting a new component in the master component list seems to help.
11. Glitchy compenent location: while designing a Yor medium class ship, a few of the 'extras' components I added would get added in a completely wrong location. I didn't 'miss' the spot and click something nearby, it just got it totally and surprisingly wrong.