I seem to start running into this problem after I have a dozen or so large fleets on the map.
When you finish moving a unit, the game will autoselect another nearby unit. If I then click on the next unit that I want to move, it will move both the autoselected unit and the newly selected unit. This can get pretty frustrating when the autoselected unit is a defensive one at a starbase that then ends up getting wiped out the next turn. The net effect is that it is very frustrating to move large fleets.
