Flemming,
Is it possible you have found a bug with autopilot movement or how autoturn acts when "skip ships with moves left" is on?
Intuitively, how it should work is: when all ships not on autopilot have been handled by the player ships on autopilot are supposed to be moved automatically. When all of the ships on autopilot have been moved the game goes into the next turn phase IF autoturn is on, otherwise it stops and waits for the player to press the "turn" button.
Ships on autopilot that reach their destination before expending all of their move points are supposed to be presented to the player. If autoturn is on they should be presented to the player BEFORE the game goes into the next turn phasen. The player is supposed to have an oportuninty to use the remaining move points at that time.
If the player presses the "turn" button at any time, ships not on autopilot with moves left are skipped if the option "skip ships with moves left" is on and proceed to the autopilot phase. If "skip ships with move points" is off, next turn is supposed to display each ship with move points left and change the "next" button to a "skip" button. If the player uses up the move points or uses up the ship (loses a battle, colonizes a planet, or conquers a planet) or presses the "skip" button then the game is supposed to look for the next ship with move points left.
If "skip ships with move points left" is on, then pressing the turn button at any time will do just that. Ships not on autopilot with moves left will e skipped, ships on autopilot will be moved but what happens to those reaching their destination I am unsure of. I would expect them to be presented to the player, but Cari or Brad may have to clarify that, and that may be where a bug is.
The interaction of all of these options and the multithreading of the game makes this rather coomplex. Hence, careful testing of all of these options and operations is needed to determine just what really is happening. I am fairly certain that the options autoturn off and "skip ships with moves left" off work correctly, as these are the options I use and I have been expecially watchful for cases where autopilot handling fails. I have been using these options mostly because these are the ones that makes it easier to detect other causes of autopilot failures to move ships.