They fixed it. They fixed it.
Left over moves on ships at the end of a turn when a ship has less than a full count for a turn are now being accounted for. After pressing the end of turn button the game moves ships on autopilot. If there are less than enough moves for a full autopilot move on the next turn the game now asks you to take action on the ship.
This is much better than it was where the game would just discard left over move points for ships that had completed their autopilot moves.
Much thanks to StarDock. This now gets rid of one of my micromanagement concerns.