The auto pilot problems that are very vexing to work around are the ones where a ship on autopilot just plain stops moving without manual intervention. The ship stays on auto pilot but stays where it is (short of its destination). There have been several threads on this problem. If the problem was simply that the ship would drop out of auto pilot before it should it would be selected by the next ship routine. When it stays on auto pilot without moving you have to run with autorun off, bring up the ship list, and click on each ship that is on autopilot to make sure it has moved (the ship list doesn't even show the correct number of moves left, shows max moves instead of 0). Then you have to take them off of autopilot one at a time and move it at least one tile manually before re-designating its destination.
Cheers,
Jack