How do I fix the pivot point of my vertex The pivot point of every vertex in the mesh of my object is out of position for some reason how do I put it back to where the geometry of my vertex actually is. I tried origin to cursor but it will say you could not do apply this in edit mode. 



As illustrated in the picture above the pivot point is far from where the vertex is located.
This is because the armature modifier is not taken into account (this is intended behavior), so the pivot point is at the non modified location of the selection.

This becomes obvious when toggling Modified edit cage (the triangle icon on the modifier):



To make things more manageable, try disabling the modifier in edit mode:



Also see Why is vertex snapping with auto merge enabled not merging vertices?