When you have ships on auto move and click "Turn" you lose any extra movement points those ships might have because the next player starts moving their ships.
For instance, I have a ship moving to a location 1.5 days away. I hit Turn, it moves it's full MP. I hit End Turn again and it moves to the location selected, but it still has movement points available. But due to the programming I can't use up that ship's extra MPs because the Yor (or whoever) are now taking their turn.
It seems to me that before the next player start moving their ships, the computer should auto select all of my ships that have movement points left and allow me to move them further or skip them. But maybe there's a reason for it being the way it is?