This is some highly annoying issue, which has been in the game at least since 1.1:
Sometimes freshly built ships being sent to the colony rally point get launched from orbit, but do not have their autopilot set. They just hang around in front of the colony. Rather annoying to find that there are 20 ships in various places doing nothing instead of flying to the rally point. The whole point of those rally points is that you can just set them and not give each new ship an order to go someplace.
