Since I started a new game with Crusade 2.2 (the last opt-in though that also listed version number 2.2, the official 2.2 update came 1 day later and i didn't want to start over again ...) I began taking notes so that I can keep track of the bugs still present (or new 
). Here what I found so far (I'm around turn 150 now and have only met one single other civ (ludicrous map, all AIs gifted, about 20 AIs, slow pacing, very slow research):
- "Need more administrators to build more starbases" notice still doesn't disappear (still in 2.2.1)
- Ship maintenance is still displayed as 0 for every ship in ship designer (still in 2.3 opt-in)
- Legions multiplication bug? I have no war yet, so I cannot say for sure, but the patch notes didn't mention this (quite serious) bug. (fixed in 2.3 opt-in)
- "Leaps and bounds" anomaly does still nothing that I can see (still in 2.3 opt-in)
- Temple of Enlightenment (Benevolent/Enligthenment III) tooltip still says 200% bonus to colony's research instead of 33%; benevolent per turn is also off (solved in 2.3 opt-in)
- Basic Laser has the same stats as Laser, but needs more space and 1 Elerium (see below, posts #8 and #9)
- Event "Antimatter Weapon": I chose malevolent and the tooltips says "+5 missile attack to every ship", but I can't find any ship with increased missile attack, neither among my existing ships nor in the designer.
- Colonize events don't happen every time you colonize a planet in a new system. Maybe that's intentional and there is a certain high, but not 100, percentage that these events happen. I also do not exactly know what should happen if you colonize the second, third, ... planet in a system. (still in 2.2.1) (Frogboy posted (see #47) that it's intended like that, colonize events are random.
- That old bug that ships being ordered to travel a long distance don't clear all FOW on their way (unless they are on the screen when moving) still persists. My assumption is still that it happens when the speed of the ship exceeds the sensor range so that the movement algorithm teleports them to the end of their movement allowance at the end of turn and only then checks sensor range. (still in 2.3 opt-in)
- In Diplomacy -> Treaty Detail it lists Resource payments still as "New Game" (still in 2.3 opt-in).
- I still see nowhere the effect of a Free Trade Agreement or any other treaty on my empire (so that I cannot check whether they now work in both directions or still only in favour of the receiver).
- Transport loading screen is still completely black with just the slider to load the number of legions.
- I can now also confirm that the legion multiplication bug still persists (that's when you invade a planet with x surviving legions and start the transporter thereafter the surviving legions are added to the transporter, but not deducted from the global legion count). (fixed in 2.3 opt-in)
- The commander bug still persists. In my game the commander gives 25% logistics bonus to my 48 logistics what makes 60. I could actually build one fleet with 60 logistics points and thought the bug was squashed, but now I trained my second commander and cannot bring my fleet to over 55 points (at least not by trying to merge on 5 logistics ship into the fleet). (at first seemed to be fixed in 2.3 opt-in, but occured again with my second commander)
- Tooltip of Subspace Resonator-P (that you get through an event) says "Drive Mass" and "Drive System Cost" although it's a sensor.
- The build time displayed for missions like Treasure Hunt on the left side in the Shipyard screen still differ, sometimes very significantly, from the time displayed in the build queue after you select the mission. (seems to be solved in 2.3 opt-in)
- Elevation Foundation tooltip says +100% Morale and a benevolent point every 2 turns, stats say Morale +25% and benevolent point every 5 turns (still in 2.3 opt-in).
- (2.3 opt-in) Movement display of currenly selected ship remains 0 after turn change. This is only cosmetic, the ship can move as usual nonetheless, but it's irritating.
- (2.3 opt-in) Research Treaty effects of received treaty are nowhere to be seen.
- (2.3 opt-in) When I have a fleet that contains a transport with legions then suddenly all ships in the Ship Designer now show a line that shows "Legions carried 5".
- (2.3 opt-in) When my fleet hit a Precursor Anomaly in the pseudo turn that resolves all the ships with movement left the battle screen was shown, but nothing else happened. The fleet was the last one with moves left, the turn was resolved thereafter (doing all AI stuff and movements), and in the next regular turn the Anomaly was still there, but when I tried to enter it nothing happened. I had to leave the game and reload, then I could enter the Anomaly and properly fight the defenders.
- (2.3 opt-in) Mercenary The Fissure: Description says Logistics 2, stats say Logistics 5.