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This can happen if you end up with the book on the device twice, something that is easy to do when hacking metadata. For example, because the author is in the default save path, if you change the author then the book will go to a new folder.
If calibre put the books on the device, it can usually find all the copies. You can check one of the books by using the function 'Remove matching books from device'. Connect the Nook, wait for the 'ondevice' field to show, then in the library view right-click on a suspect book, bring up the submenu under 'Remove books', and select 'Remove matching books from device'. A dialog will appear showing all the copies of the book that Calibre knows about. Delete the wrong ones.
Another sledgehammer (but more certain) approach is to delete all the books and resend the ones you want.
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