Alright, I thought it would be cool to just collect all the latest bugs in short in one place:
These are known to me (playing as Yor):
1.The sounds and music are breaking if there are too quick changes between management windows. Sometimes the game goes completely silent, sometimes a screen associated music will get stuck and play all along everywhere, infinitely. (only reloading fixes these) SFX sounds can only be turned off, but not set to be more silent.
2. Anomaly artifacts are rushing planetary projects, like Assembly, when they should skip those.
3. Some improvements will not update / and can't be upgraded (or missing) like Manufacturing Yor, which stops at the second tier (Manuf. Collective).
4. Terraforming can only be unlocked until the second tech (Terraforming Plant) at least at Yor, because Extreme Colonization is blocking the way (disabled). These two branches should be separated or spinned-off.
5. Starbases and shipyards still seem to only have numbers at their weapons and defenses, but no actual damage are done by them to my ships (tried several times, but my crafts are unharmed). They can be picked off easily by a single shot.
6. Weapons fire and explosion effects only occur randomly, most of the time are missing. Especially at starbase/shipyard attack, and at planets (though this latter might be intentional).
7. At U.P. screen your own bar in the corner is empty, no actual percentage value can be seen. (you have to remember it)
8. Sometimes the turn right after you defeat an enemy, or you reload the game, already dead enemies can be contacted through diplomacy and you can get treaties/techs from them. (This might be a bug. However I personally like this feature that the leaders/race are not completely gone after you eradicate them.)
9. If an anomaly is inside or near a nebula/dust cloud, the survey ship will not collect it manually, only if "auto survey" is set. Instead the ship goes into the middle of the cloud.
10. A.I. survey ships sometimes go on the tile of an anomaly without actually getting it, and they get stuck there.
11. No matter how is my relationship with other races (even if I am at war with them), they still sell their own fighters and other things to me very cheap. I can buy off my opponents' military basically.
12. At Yor the Assembly project seems too easy to exploit. It gives a fix rate of growth no matter what, even if I set social production to only 1%. The result is that I can "grow" all the time without any disadvantage and still building ships, except that there is no planetary building. I think this should be harder, so that you have to spend a reasonable amount of your production to create Yor, maybe the more % the more growth rate (still constant - linear). This way you can barely feel any difference playing as Yor, as growth is as easy as 1%.
13. Now maybe I'm wrong about this one, but as I saw permanently passed terms at U.P. sometimes a few blacks-out in the list, therefore I can't change or repeal them, but later on becomes available. - this has to be further investigated.
14. I don't know yet if this is only Yor specific, or it is missing from all the other races too, but the techs are missing which could increase the range-effect on starbases. Maybe this was intentional? Still, this way a generic starbase can not be turned into any specific type, if it currently does not cover a resource or planet. (It was a strategy to pre-plan their placements and extend their ranges later on.)
15. If a Transport ship is ejected from a planet orbit, instead of the shipyard, the select population screen pops up but blacked out, therefore you can't assign people on them, ejecting the ship empty. (Check if this occurs with Colony ships too, or when ejecting from Shipyard.) There in no problem the first time these ships are built.
16. Ships are avoiding to pass through shipyards, while they cross starbases. Is this intentional?
17. In asteroid fields, nebulas and stuck-in-anomalies, ships can't be seen (disappear), as they are overwritten by the texture of these objects. You can only find them if you know they supposed to be somewhere there.
18. Still problems with instant-updating tech research turns (NA), building queues after production wheel set (NA), and on maps resource lines (ex: destroyed mining starbases).
19. !!! For some reason, even if I set Events to be Frequent, once all the planets were colonized, a global event only occurred once, therefore I can't go further in the Ideology tree. Yes, more than 100 turns have passed, but events just stopped activating randomly.
20. I know this is minor, but in many cases the floating text boxes do not fit the texts inside them. A good example is at dust clouds / nebulas.
+ Conquest Victory can be hardly achieved if killing all your opponents fills up almost the entire map with your influence. In only 10 turns, Influence victory will be earned first. How is this conflict is going to be resolved?
Overall: Because of some of the aforementioned major bugs that are altering gameplay significantly, it currently gives me the feeling/impression that the game is now somewhat worse than Beta 2 was.
However I remain pretty enthusiastic about it, because I love the game sooo much, so keep up the great work! 
Feel free to add more to the list!