@Andrew, thanks. I just tried that and still nothing. In order to see my documents in ~/Library/Mobile Documents/ it looks like I have to tick the box to search for home and live with the inclusion of mail attachments. I'm tempted to do a fresh reinstall of Alfred to see if that will fix the problem.
I did that. After adding each folder individually, the error did not come back. Also, the results in the documents folder (~/Library/Mobile Documents) were no longer visible. They only become visible when checking the include folders in Home box, but then all the mail attachments show up again.