I can't reproduce this.  I did a test with:

Layout:
/tmp/ddtest/source/hello
/tmp/ddtest/source/lost+found

Included:
/tmp/ddtest/source

Excluded:
/tmp/ddtest/source/lost+found

After a backup & restore, only hello was backed up and restored, as I
would expect.

Can you give more info about your setup, so I can try and reproduce?

** Changed in: deja-dup (Ubuntu)
       Status: New => Incomplete

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https://bugs.launchpad.net/bugs/953194

Title:
  deja-dup attempts to backup "lost+found"

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