Why are incoming mails saved twice?

[Hermann]

Hi,
I use nnml as mail backend, and I figured out that arriving mails are
stored twice:
In ~/Mail/mail/misc with numbers and in
~/Mail as Incoming*.
When I clean up my inbox, those Incoming* mails still exist.
Is there a way to get rid of them without destroying the structure of
mail handling? Simply deleting all this mails is perhaps no good idea?
Hermann