1. As long as the research is queued, you can queue something to build/upgrade, but it won't actually start until the research is done. What's odd, however, is the Starbase not ignoring the upgrade it can't begin and working on the others first.
As for losing the planet to culture, yes, intended, Auxilliary Government stops you losing the planet to bombardment, not culture.
3. Was it an Advent player and if so, were you blowing up their Trade Drones? They have a tech that applies bounty to anyone who does that.
4. That's because the Vasari haven't been added yet.
6. I'm not familiar with the map, so I won't comment.