If you have all the available plugins installed, sometimes the Ignoble Epub and Inept Epub plugins conflict, and if that happens, you will need to disable which ever is not the right one for your ebook, remove the book from Calibre and then import it again.
I find this mainly happens when I import books bought from Barnes & Noble. So I just disable the Inept plugin and then enable it again once the B&N book has been successfully imported.
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