When a subsurface modifier is added to a model, the surface "pulls away" from the true vertices of the model. A small protrusion like you have will show an extreme case of this, while on the gentle curved area you can see a small gap between your vertices and the surface of your object.
At the top of all modifier panels you will see buttons that control the display of the changes the modifier makes. The first two apply to the render and object mode viewport display, the last two show the effect in edit mode and the deformed edit mesh. All modifiers have the first two display options while some do not have the third or fourth.
By enabling the last item (the triangle) your vertices will snap to the deformed surface. Disabling the third button (the cube and vertices) will hide the deformed mesh so you can only see the true vertex and face positions.