Noticed with 1.3 (newest), if I invade a planet and they have terraforming type improvements going, upon winning those tiles disappear and can't be terraformed.
Also is the bug were you get a planet by influence, and you goto the starport and the game jumps to the next planet you win by influence ever going to be fixed ?
Also annoying is when you have a tranport get to a planet on the end-of-turn via autopilot. After winning, you usually can't pick a ship to build.
Influence wins should probably be changed to queue up an event in the pop-ups. That way when I want to deal with it, I'll click it.
And another annoying bug is when the AI decides to talk to you, but doesn't say anything. (ussually after a load.)