1. I think this has been resolved internally, but my flagship disappeared in a star's well. I can't see it and it won't move. (Maybe resolved as of v2a)
2. Militia Weaponry didn't increase the "Average Gauss Damage" statistic for Gauss Platforms. I don't know if the damage was actually increased...it also doesn't increase weapon damage on ships in friendly territory as advertised. (still exists in v2a)
3. I captured the Occupied Planet in a 4 player FFA match vs hard AI and the remaining two AI never attacked it (other than a single Novalith firing at it). They weren't even on their way because I was monitoring three jumps out. (still exists in v2a).

Will add more if I find anything...