Ok, I don't know if anyone else has had this issue. It has been in the game since the original Gal Civ II, but seems to have gotten worse in ToA. Any time I try to upgrade a starbase of any kind with a fleet of constructors, I have to do it twice. The first time the fleet reaches the starbase, I get the popup window asking me what upgrades I want to make, and when I accept the first one, the window goes away and my fleet sits on top of the starbase. What's more, my fleet's total moves have been reset to the original amount. I then must move my fleet away from the starbase and do the procedure again, sometimes TWICE.
Has anyone else had this issue? It only seems to happen with fleets of constructors, not individual ones.