I think if u go to shaded mode then u will see a face is covering the hole where nth was suppose to present.
If it is it then, it is one of the most irritating problem.
one solution of this problem might be this:
use the split poly tool with several "Divisions" level(10 or higher, depends on the complexity of ur model).The relocate the vertex to make a curvature look along the path which u will cut the face to make the hole.Use as many split poly tool as needed.(try to limit the number the division level with respect to the vertex of the main object.otherwise model could turn out messy)
Then delete the central face to make the hole.Then merge the new vertex with the old one of the object.
This solution might be a little weird.But it works!
one tip while trying to move vertex on a certain plane in perspective view:
Click on the axis which u wanna lock(After selecting the MOVE tool), then use the middle button to move it.