If you have two vertex you want to merge to one:
just select one of the vertex, move it somewhere out of the way, hold down crtl+v and snap it to the other vertex(hopefully still in the original/desired position), then merge the two vertex together.
Its not wise to try and merge three or more vertex at the same time, just try do it two at a time and make sure its right.
Thanks for wasting your time reading this line.