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,
