[BUG] Stuck on idle and cannot end turn due to unit in stack being upgraded and another still with moves

I have seen this too. It seems as if the game picks a ship with moves left, then if it is a stack, selects which ever ship it thinks is first in the list, The game should not do this. However, I have discovered a work-around for the time being that lets us get past this problem: click on the stack and you will see the selected ship change. Do this until you have the ship with moves left, then move the ship. This gets past the bug.

Edit -- I have also tried to select the ship from within the ship stack display (bottom left of your screen shot) but found it was not very intuitive. I didn't seem to be able to get the correct ship that way,

Thanks for posting your issue. Would you kindly, submit a ticket via our support system so that I can better assist you with your issue. After following the link, run the support tool, describe the issue you are having and then send us the zip file to greatly speed up the process!

Link to forums for explanation:

https://forums.galciv3.com/452855/page/1/

Link to support tool:

http://sd.stardock.com/Support/supportToolTest/SDSupportTool.exe

Workaround: disband any fleets, move any ships with moves left off the tile. I have had to do this a few times.