losing moves

Same here. Another possible side effect of this seems to be several times when I start to move a constructor into place and try to build a starbase--- the option is not greyed out, but when I click on build starbase it tells me it's not my turn. I have to end the turn and wait.

Yup, forgot this one but have also seen it

I think what you see is the new mrechanic in Crusade that actually prevents losing moves

Before Crusade it was so that if your ship that was sent to a remote spot had moves left when that spot was reached those moves were lost because you would gain control back to that ship only in the next turn. Since Crusade it's like that: if there are ships ending their automatic movement with moves left at the end of the turn (after you press the Turn button) then the game will stop in kind of mid-turn and let you cycle through all ships with that condition. You can then use up all remaining movement on those ships, but when you do that with the last of those ships the AI turn starts immediately without you being required to press the Turn button again.

I hope that was halfway coherent

Edit: and yes, if you open the command menu of a constructor in such a mid-turn, *but after the AI turn has already resumed*, you get that message about it's not your turn etc.

Maybe this is also behind the 'alien x wants to talk to you but are currently trading with someone else/wait or decline' messages.