I have a few more points, but this time without screenshots - I promise.
A:
I noticed the same message about advancement in espionage towards some race popping up twice in consecutive turns. This happens in ~50% of the cases an advancement takes place, regardless which race is concerned.
[Besides, if I start espionage on multiple races the same turn to the same degree (BC), these steps will happen EXACTLY in the same turn until 'advanced' is finally reached. Call me dumb, but this sucks. There should be at least some minor element of chance in that...]
B:
In the Negotiations Screen the terran ambassador once suggested to 'quietly supply arms and ships to all races currently at war with the fierce Drengins' (or something like that). Sadly, he was talking to the only race *existing* besides his own and the Drengin, and there were no wars going on at this time...
C:
If you chose neutral alignment one of the effects should be to have all starbase upgrades instantly available, once they are researched, iirc. This works for weapon upgrades (Ship Pounder, Star Javelin, ...), but doesn't work for defenses (Ray Shielding, Combat Armor, ...)
D:
There are descriptions to 'wonders' that do not match their real effects (especially MCC), but I think you know by now...

E:
A few times I noticed different values for remaining build time for a planetary improvement (Colony Screen vs. Civilization Manager).
F:
When entering the window for upgrading a ship, you are not only able to upgrade an existing (undamaged!) vessel to EXACTLY the same ship type, but this also costs you money and time...
Thanks again,
swh.