The missing piece is called a "plaster guard", used to keep plaster and etc. out of the vavle area while the wall is being finished. They can be and often are removed prior to tiling.
The person who roughed in the valves did not position them correctly; they should have been installed deeper into the wall. The problem with pulling the valve is that any attached rigid piping (copper, not pex) such as supply lines or the shower riser will also need to move.