I have a tank model, which consists of a tank body and a turret. I also have an empty gameobject that I am using to adjust the turrets center of rotation. The turret is child to the adjustment object, and the adjustment object and tank body are both children to the tank prefab. My problem is that when I move the turret, I expect the adjustment gameobject (its parent) to not move with it, but it does!
If you have the scene's tool handle set to be at the center of the selection, it can seem like the empty GameObject moves. Try changing it to pivot and have your adjustment GameObject selected when your turret moves to see whether it really moves or not.