I've started encountering this a lot. If I have a fleet or ship next to a ship that is getting upgraded, sometimes I can not move it. The ship/fleet is targetable and shows that it has moves but just won't move. I was just moving a fleet of troop ships and when it moved next to a ship that I had just put into upgrade the troop fleet got stuck and I can not move em anymore. Not too big an issue for me as I usually only do upgrades that take a week, but definitely a bug.

Well, the problem is worse than i thought, at the end of the turn, I kept trying to move the fleet with the arrow keys and the game crashed, won't do that again. But advantage me -- extra round of ship moves I get reloading the game will make my attack much better when I replay.