Some of these are things that need to be cleaned up in the beta process;
When playing as Altarian, you do not get multiple uses of "biosphere manipulator" for terraforming. It works only once yet the description indicates that it should be able to be used repeatedly. The equivalent feature when playing as human does work repeatedly.
If you take over a planet from another species and there are still ships in orbit around the planet (defending) you cannot control them, upgrade them or kick them out. They still belong to the alien species, even if that species has essentially been conquered.
Under weapons techs there are still quite a few "Not in Alpha" weapons (pulse cannons, graviton drivers, quantum drivers).
Throughout the game there are still areas that do not have descriptions (improvements, weapons, ships).
Sometimes the borders between areas of influence do not line up. You get a little crescent moon image where the two ends do not line up.
There are some times where there are visual artifacts in certain hex shapes.
The lines and visual artifacts are not video driver issues. They are very specific to that individual little hex shape and persist in that exact same location, no matter what the zoom factor or if you pan away and then back to that area. Those things will still be in that spot. I do have screen captures of these if they are needed.
Game behavior of ships "exploring"; If you end up with a collection of random ships that you "discovered" and you set them to explore, after a period of time they tend to form swarms or fleets by themselves instead of acting independently. If you do not pay attention to these ships that are out "exploring" they often end up in some obscure corner of the game, doing nothing, even when there are still things and areas to explore.
Sometimes when you select a planetary tech to be "rushed" the game will get stuck on that particular tech for that planet. The only recourse is to go back to that planet and to delete that tech and to re-select it. That seems to kick the game back in gear.