1 - when ships are attacking some star bases or shipyards at mid range, their beams are hitting them, but in most cases hitting them in empty air in four opposite corners. the problem seems to happen when your ships are in medium range, in close range it dosnt seem to happen. It could be that all the beams are just missing. but because its hitting the 4 corners its kinda looks strange. The example in the pic is a Yor Starbase in case its an issue with just that one (See Pic 1)

2 -  When you change battle speed when paused all the beams (and not sure about other weapons) instantly reverse 180 degrees (see pic 2)
 
3 - Some shipyards and starbases have all there attacks emanating from the center of them (actually only noticed it on the Yor shipyard so far), basically making it look like they are appearing out of thin air, instead of starting at various random points on the surface of them.

4 - Star bases still spin when the battle is paused, I haven't looked but im guessing this might affect any animation on ships.

5 - Maybe not exactly a bug, but when defending a shipyard or starbase, there is no ship class that will stay around the base. they will fly way ahead, in most cases just getting killed as the enemies ships stay out of range of the bases while they are dog fighting. Although in some cases you might want this to happen, I want the option for them to stay close as well. I'm guessing the distance issue is partly due to the fact that starbases and shipyards cant move on the battle field.

I want a Defend option that will make them stay right next to the shipyard or star base... unless there is an option or class I cant tell. the descriptions for the classes don't clearly explain what one I would need, I mostly tried guardian where it says it will hang back but it didn't work.

6 - The " upgrade design to latest version" button in the shipyard doesn't work in most cases, if at all. This mostly is just an issue with custom ships you have made. All it seems to do it change it to a random constructor.
 
 These last two more annoyance then bugs.
 
7 - This has been mentioned before, but upgrading a ship on the map cost is still WAY to high. I was building a ship and before it finished I got new sensors so decided to add it to the design, it only cost like 6 extra manufacturing then the previous build, but because as above I couldn't upgrade in the shipyard I had to wait until it was finished. it ended up costing me like 500 credits to upgrade it.. was easier to just destroy it and build a new one.

8 - There is no easy way to repair a starbase or shipyard. You should be able to use a constructor to repair it. You use to be able to do it for starbases in gal civ 2.