Here's my short list of mystery bugs and issues. I played a metaverse game (though apparently I botched getting the score uploaded), Begginer level, Medium size universe, 9 races, I played stock Thalans. (game ran from about 7pm to 3:30am... god... it's been years since I lost track of time that badly! Good job!)
1. I too am getting the "They blew up my resource mining starbase and now when I try to build a new starbase on that resource, the game acts like it's not there any more" bug. (Did not try to save and re-load to correct issue.
2. I'm clicking on ships and fleets and/or fleet remnants (fleets that lost one or more ships but are still fleets), and it's refusing to combine them up to my full point total (i.e. a 5 point ship and a 10 point fleet, my cap is 20, but they won't combine into a 15 point fleet)
2.1 Clicking on two ships that have come from different locations, but have been moved onto the same spot, will not combine into a fleet. Instead, I get a new fleet with no image on the list of ships/fleets in the window below, and has a point total of zero. Repeated clicking just generates more of these zero point fleets.
2.2 When dealing on a tile with multiple ships and/or ships and fleets, you cannot click on a fleet icon and disband that fleet without moving it into a separate spot on the map first, and then moving the individual ships back into the stacked ships spot.
2.2.1 When you are on a tile with multiple ships and/or ships and fleets, you cannot get a breakdown of the individual ships in a particular fleet until you move the fleet into a spot where it's the only ship/group of ships on the tile.
3. Only saw this once, and I didn't pay close enough attention to it to be absolutely sure, but I won a close invasion battle on an enemy held planet, won it (with very few troops left), but did not capture the planet.
4. I am experiencing the "removed components come back when you click on a second component to remove" bug when upgrading an existing ship design.
5. Not sure if this is a bug, but somewhere along the mass driver tech tree, I found myself able to select nano-ripper guns. Later in the game, they vanished. (I *think* this may have occurred after I lost a planet I had invaded.. I'm guessing nano-rippers might be something like that unique ship armor building you can create early on?). When I retook the planet, I did not recover the nano-ripper build item for any new designs, but I could still build old designs that had the rippers in them. Shouldn't I still be able to build nano-ripper equipped ships even if they're a building based item? (Otherwise, how am I able to continue to build the old designs with nano-rippers in them?) I would expect if the rippers are building based to either be able to continue building them once the tech has been added to my build options, or, any designs that use rippers would become unbuildable until the building was restored. (Though I'm not sure how that would work if it's a unique building that can't be built by others once someone else built it)
6. Alt-tabbing out of full screen mode sometimes comes back, sometimes doesn't. When it doesn't, if I hit esc a few times to get to the options screen, I can usually get the video to come back, and can continue playing.
7. Annoying AI sour grapes surrenders. (I don't know if this qualifies as a bug). 4 of 5 races that I conquered waited till I was surrounding their last planet, and then surrendered to one of the other races I was not at war with. I can see that happening occasionally, if they were allied with that race, but, it just annoyed me that I had to either leave a now foreign controlled planet in the heart of my territory, or extend the warfare to yet another race to get the planet I was after.
8. A.I. Allies make peace with me the same turn they declared war on me due to treaty obligations. I'm thinking you need to set a minimum number of turns or something before the allies will negotiate separate peace with me. I had 2 races I had good relations with, but they declared war on me after I attacked their ally, but as soon as I talked to them and offered them a straight up peace treaty that turn, presto, it was all kosher. That seems to make mutual defens/alliance treaties about worthless for the AI to make, doesn't it?
9. Precursor vessels seem to be occuring a bit too frequently? I found 2 ranger class vessels on my homeworld, the terrans found a ranger, and the Korx had *9* precursor corvettes defending the same planet. Seemed like that was an awful lot of precursor tech to be floating around intact on people's homeworlds. I am guessing that the precursor big ships are really supposed to be rare occurances to give a race a boost when it's needing a little extra oomph. (A suggestion: Give the option to dismantle the ship for one or more technological advancements due to reverse engineering. one Ranger *is* pretty spiffy, but salvaging a new weapon system, defense system, or specialty pod that could then be put into production would be really cool too, and more reasonable than finding an intact, spaceworthy vessel buried on your planet after how many hundreds of thousands of years?

(just a suggestion))
As I'm still a bit tired from playing, those're all I can clearly remember. The fleet management ones were most frustrating, since I couldn't combine fleets and had a lot of single ship battles that I didn't want to have. I could never tell when a group of ships would or would not combine properly, and having to make them move off the stack square to review/inspect/or ungroup/re-organize my fleets was not good.