5/ Mentioned in another thread but I also hit on this numerous times - capital buildings sometimes are unplaceable after cultural takeover of a planet. Capital building shows on the build list, but can't be placed.
6/ Queued build orders in shipyards often fail for no reason, particularly queuing up station modules. I couldn't figure out why I kept having to go through 10 different shipyards queuing up 10 or so orders every turn. Turns out they just fail after the first build. Same thing sometimes happens with the repeat order toggle, it just builds one thing anyways and quits. Note these were not items using special resources (which should be spent anyways when you queue them up).
7/ Lots of missing functionality with the Civilization builder, even with the expansion pack for it. In particular, you can't choose your 4 special factions for your Civ, nor do you know what they even are. Many special stats for species are also hidden, such as level of criminality or how well they get along with other species.
8/ Flavor text is often Civ specific, even for generic choices. In particular some techs and hero ships. Minor nitpick, but someone should do a pass on that and reword or replace with variable strings.
