Ok, got a few here:
You need more research stations for higher tiers of research. I like this idea a lot however the research descriptions need to be updated to reflect this additional requirement. Also, you are unable to queue up higher tier research topics until the second (or more) research station is
completed. Probably should be able to begin queuing topics once the next research station is queued (like you can start queuing research topics when the first station is queued but not finished yet).
Enemy ships seem to get goofy when you build a phase space inhibitor when they already have orders to jump. They will just idle there and some even drift all over the place:




In this one you can see that the phase inhibitor is still under construction ( I thought I got a better screenie of it but I guess I missed, but in this one you can still see the two lines under its icon indicating that it's still being built) yet the enemy fleet is inhibited.
And a couple minor graphical glitches:

After destroying an enemy frigate factory that was in the process of building a frigate, the spark effect persisted for a few seconds after the factory itself was already gone.

Just before I wiped out their last colony, these guys offered me an alliance. I didn't take them up on their offer and when they died the hand icon remained. Notice in the screenshot that their name is greyed out indicating that they have been eliminated. The hands never went away (no, you can't click them to accept the alliance offer). Haven't tried to reload the save game and see if it is still there or not.
On the plus side, I haven't had a crash yet