This only happens when you copy/paste textured things (or when you have previously copied and pasted something). If you copy something untextured, this doesn't happen, unless you have previously copied a textured object. If you have to copy a textured object, do so, but only paste that item. If you need to copy something else, close MED and reopen it and your file to prevent this from getting out of hand. I have one model with over 4 million skin vertices because of this, but barely 1500 model vertices and 3000 faces.

What is needed is to be able to delete all unattached/unused vertices in the skin edittor.