I've found several times that stacked ships with moves left can be hard to manually move. I've had to unstack the ships to move them properly. This is not always a good thing because the right ship may not be the one that you are allowed to move. You have to let the "idle ship" button even select one of the ships/fleets. It won't always let you go through the stack.
If there is another way, it must be awkward to activate. I tried all manner of clicks but nothing seemed the right thing or repeatable.