I wonder if it's because they get confused. When I see someone in a turret in the back of a warthog I instinctively think "oh, he wants someone to drive him around, I'll be the nice guy and do the job." but then unlike some people, I take a moment to see how they're positioned and if they moved the warthog there and I know that they did, then I leave them.
A good possible way to fix this is for 343i to make the mounted turrets into a REQ item, so that you can lay down a turret and not be able to move it. They would cost either the same as or one more then the base turret REQ. (ex. machine gun turret REQ Lvl 2. mounted machine gun turret REQ Lvl 3)