These are pretty minor and I expect painful to fix, but here goes:
On loading a new game, you go through the same rigmarole as starting a game: start exploring space GNN report ("A Journey Begins"), select research, skips to planet. This feels unnecessary.
If a planet reverts to you due to influence and you go to starport, the turn start-up continues (pop-ups for build, etc.) (may have mentioned this before)
If you meet a new race and click "speak to", sometimes another race will jump up instead because it wanted to talk to you. Once you are done talking to this third party, the new race will appear.
The AI is want to throw itself against starbases (in its territory, but only a mining starbase (morale)) with no hope of success. Won a game easily because the AI wasted it's ship on my starbase instead of actually attacking me.
The AI became upset ("I know what you're doing") when all I had was freighters and a mining starbase in its territory.
Start-up text for "Battle of Gods" is the same as starting normal. It talks about building technologies, etc.
Likewise, Battle of Gods unnecessarily goes to research screen.
Hints display for disabled victory conditions. It's a little odd to read about Influence Victory when I know that's not a possible path for this game.
Have seen equal bonus for neutral and evil choices. Even more common is equivalent (+X% PQ, for small variations in X).
Perhaps by design: If one planet has an event on colonizations, all planets in that system are likely to have the same event.
"Gain Experience" anomaly doesn't appear to do anything (I expected the level of the crew to increase, or at least some bars to light-up)
When attacking heavily over-balanced ships, target selection system is suboptimum. In particular, if I have enough weapons to destory any ship with high likelihood (~60%), I should target the one with the highest expected damage, not small fighters that are easy to kill but have a few less weapons.
