Every time I save a document (Pages, Numbers, Textedit, probably more) it creates a duplicate with a tilde at the end. I could create a thousand clones by pressing save a thousand times!
Are you running 10.7 or 10.8? I did a quick google search and saw this reported on 10.7. I tried to repeat it with 10.8 & textedit, but it did not repeat.
Is there anything non-standard about your setup? Are you saving to a non-HFS+ drive, for instance?
Is it only Apple apps that do this? Is it only apps that use the new Auto-Save model?
Ah: you posted in another thread about wanting to turn off Resume. Did you bar access to the SavedState folders? If you un-do that, does the problem go away?
Is the tilde before the file extension or after it? How do the iterations of successive "saves" alter the filenames of the duplicates? e.g. how is the second duplicate named differently from the first?