Ok, so it isn't really a problem until your ships can move about 20 spaces a turn, but how often have you accidentally clicked too far and set your ship on autopilot, so you have to search for it and deactivate it?
I think the map should show the possible movement area of ships (highlighted line, like the life support one).
Alternatively, set an option for the ship called "No Autopilot", so autopilot automatically disables itself at the end of the turn. Perhaps in the main menu we could choose to enable/disable this by default for new ships.