I have noticed this quite often and it is easily reproducable.
1) Have a bunch of ships flying to Rally Point A.
2) Go to the governer screen, select all ships going to Rally Point A and tell them to go to Rally Point B.
3) Notice the "Autopilot" turns off under all the ships. Notice they all still have movement.
4) Press Turn. Notice none of the ships moved, wasting that turn of movement.
5) Press Turn again. Notice autopilot turns on and they all move to the new coordinates.
Obviously it is missing a turn off movement. This is really annoying when something is time critical, it means I have to update every ship destination by hand so that turn isn't wasted.