I went home on my lunch break but could not duplicate the vertex problem. Is there any chance you were extruding an edge on a face that you previously extruded, before you selected keep faces together. If so, then perhaps that's where the extra vertices came from.

Just for kicks and grins, create a polygon box. Select an edge and extrude it. Then check to see if the vertices are still multiplying on you. If not, then it may have just been from the extra unwanted faces created earlier.