Ok, so here are a couple of bugs that are very (very very) annoying.
1. The hyper warp drive (first version) does not have the hardpoint in the center, it is off to the side a bit which causes symmetrical issues.
2. If you build a super structure (only one allowed per planet, ie fusion reactor) but decommision it before it is built, you are not able to build another one. Actually I just tested, even if it is built and decommisioned later, you can't build another one.
3. The custom oponent sliders under the personality tab do not work correctly. It seems that once the alignment is set and you leave the screen, you will not be able to change it again unless you create a new race. Also the other sliders seem bugged as well. If you set the resource slider and leave the screen, it will change to something else. It may be tied to the difficulty level, but dropping another bar to compensate does not help, it just does more wierd stuff (ie going to another setting or ignoring the setting that was changed.
In my opinion these need fixed.