I've had numerous fuel issues with my survey vessels, usually because I use FAC-sized ships.
I think what happens is that the movement happens, then the conditional orders are evaluated. What invariably happens is that a ship is at 31%, it goes through a day's maneuvering or 5 days maneuvering, and now it's down to 20%, time to go back for refueling but now we're too far away to make it.
A conditional order of 50% fuel would be very handy for FACs and fighters - because if you get to the halfway point, it's time to go back!