The only two ways I'm aware of doing this are:
Rename, Move, and Copy tool.
Handheld Sync tool, set to copy to a directory structure.
You can also create copies by drag-dropping from MC's UI onto Windows Explorer (or the Finder in OSX). It doesn't do a directory structure or anything when you do that, though, and just copies whatever is selected to wherever you drop them. I suppose it is possible the OP drug them onto the root of her/his NAS or something? That doesn't seem likely, but possible.
Also, it isn't relevant to this discussion at all, but you can also
move and rename files by directly editing the [Filename] tag.
So, if you have a file here:
M:\Audio\Music\B\The Beatles\Abbey Road\01 - Come Together.flac
And you directly edit the [Filename] tag (in the Action Window, for example, or inline in a details view) and type in:
C:\foo.txt
If the original file exists on disk, MC will
move the file to the root of the C drive and rename it foo.txt (which will break the file in all other applications because it isn't a text file), ala Rename mode in RMCF. If the original file does
not exist on disk, it will just update the link (ala RMCF in Update Database Only mode).
In fact, in days of yore, there
was no Find & Replace template in RMCF, and the way you did it was with the regular Find & Replace Tool and just edited the [Filename] field directly. We were like savages poking our computers with sticks.
It
isn't possible to create duplicates this way though, so it is unrelated here, but just worth throwing out there for general knowledge.