Running 1.01 now:
1) Ship movement points in fleet is missing
2) Launching ships from a shipyard which requires you to select how much population does not tell you what type of ship it is for!! I launch colony ships with 0.5 units of population while I launch transports with 2.5 - 6 units of population. Unfortunately, I can never tell which type of ship it is asking about!
3) AI declares war before they can even attack me. I mean, seriously, why would you declare war on someone who can reach your colonies when you cannot reach their colonies in return? And why would you declare war on someone if you don't have any ships to fight with? And why declare war on me when you have no troop transports to actually be able to take one of my colonies? This is challenging difficulty, but that just seems silly. They declare war and then I spend 100 turns researching various techs and build some carriers and go stomp on them right as their first troop transports start heading towards my planets without any battles in between. I consider this a massive AI bug as it tips their hand way too early and makes it easier, not harder.
4) AI sends colony ships to colonize new planets they have never explored. Again, this is challenging difficulty, but this seems like out-right cheating on the part of the AI. They never sent a single ship to go inspect the system, but then send a colony ship directly to the only colonizable planet in the area? How is that possible?
5) AI seems to know where my ships are, even though I should be well outside their sensor range. Not far into one game, a civ declared war on me and was sending ships to attack my ships and kept adjusting course to target my ships even though they didn't have the sensor range to be able to see my ships. They were attacking one of my "sensor boats" and their ship was at the edge of the sensor boat's range. I had researched higher sensor tech than they had, and my ship was the same size hull but had nothing but sensors on it. Still, they seemed to always know where it was and always headed right for it, turn after turn. Blatant cheating on the part of the AI does not make the game fun or strategic by any means.
6) On challenging difficulty, the Altarians are able to out-produce, out-research, and out-population me despite my custom race having +2 to production, research, growth, and food with -20% maintenance costs and choosing prolific and intuitive and using the Altarian tech tree while sending out colony ships as fast as I can build them and building only factories and research labs. I can understand them getting some extra difficulty bonus to one thing (like research) but to out produce, out grow, and out research me they must be getting across-the-board bonuses which are quite hefty. In every game I start, they are either always in the lead on all those things or they are only just barely second in one of them to the Kryn and otherwise in the lead on the rest. That seems a little unbalanced and overpowered for one race to be so heavily leading in all of those aspects. At least vs the Kryn I can keep ahead of them in research and/or population and/or production, depending on the game. The other races I have no problem staying ahead of in most games, unless they get some lucky starting position and I get an unlucky one.
7) Start positions need some balancing. I had an immense game on a spiral galaxy where I started near the edge of the core where I explored every star system outward from my origin and by turn 60, still had not found another colonizable world. My ships had explored all but 4 star systems within range. I ended the game and started a new one and by turn 46 had 14 worlds colonized. That is an enormous difference between the two and should never occur.