1) I am not positive, but going from memory I believe this was actually fine in 1.0, and then became broken in 1.01 or 1.02. In any case, it's still broken now so I'll mention it: When making (or editing) a custom race, in the "Appearance" page, the bottom-right of the 4 horizontal selectors, "Texture 2", does NOT jump to the active value when you leave the page and come back again, or edit a difference race, or whatever. The other 3 selectors DO (Materials 1, Materials 2, Texture 1), but "Texture 2" - the bottom-right one - does not. Whenever you come back to the Appearance page, it shows the most recent value the user had ever put it on, when it should be loading the saved/active/current value of the race currently being edited. This is very annoying when trying to fine-tune ship styles for multiple custom races.
2) The 1.03 patch notes said something about Specialization Techs now having correct colors in the Tech Tree after loading a save. This is not 100% true. I am still getting some, but not all, of my already-finished specializations drawn in black after loading a Multiplayer save. If I exit and re-open the Tech Tree screen, they are then colored correctly. Kinda wonky.
3) The right-click Go-To command for ships still can, and half the time does, cause ships to go outside their range limits when pathing to the requested destination, particularly when there are obstacles involved. In some cases with long edges and steep angles, it can be used to make ships go WAY outside their range limits. I know the devs are working hard and have alrdy fixed a ton of issues, and we're grateful for that, but this one is sloppy-looking and would be a very easy thing to fix in the code.
4) I built my first Research Cloisters the other day. Then I got Quantum Understanding, and went ahead and upgraded it into a Quantum Research Foundation. Here's the problem: As soon as the upgrade finished, I noticed Research Cloisters was now available in the build list again on all my other planets. I didn't try queuing one up or actually building it, but these are SUPPOSED to be "Player Achievement - One Per Player". I'm pretty sure that having both the base and upgraded versions of the building simultaneously, using two different planets, is not intended, but it looks like the game currently allows it. If so, this would be a massive exploit given the effects they have.
5) Colonies can still reach 100% Planetary Defense stat and be immune to invasion, and the AIs will still waste their Transports and troop populations trying... This is a game-breaking situation. Also, we *sorely* miss the MOO approach where planetary defense structures exist that fight directly in ship combat. Oh well, sigh.
These last three points are not bugs per se, but I wanted to mention them anyway:
6) Lack of Insane map size availability in Multiplayer is driving us nuts. I'm well aware several things, including sensor stacking and maybe habitable planet generation, aren't even finished being worked on yet as far as scaling for map size goes, and there may have been other technical problems as well. But this is the one thing we are primarily, desperately waiting for.
7) The Thalan Tech Tree is massively, ridiculously, absurdly overpowered. I'm sorry, but it is. It's SO bad I never even bothered looking at what any of the other races get in their trees. I simply selected it for my custom race as soon as custom races were enabled for multiplayer, and have been destroying everyone else on empire stats ever since. I would recommend reducing Hives to +2 production on their base effect, and even THEN you would still need to buff all the other racial trees just to compete with the Thalan one.
8) Speaking of Thalans, I've noticed that in every single game so far, the AI Thalan player has been doing extremely poorly. I have frequently been checking in with them to see if they have a Hive Specialization tech I can trade for, and they never do. This got me thinking that possibly, the reason for their consistently low empire scores just MIGHT be that they're not researching the base Hives tech at all. That would explain why they don't ever have a follow-on Hive Spec to trade, and why they haven't been storming the galaxy with the dominance their godly racial building provides. I could easily be wrong and this could all just be a coincidence, in which case so be it, but I would recommend checking your AI XML data for Thalan-player research decisions, and set them to always always ALWAYS research Hives first. (Though technically they'd be getting it with their Intuitive ability, just like I do heh.)