Add to package line:
Code:
<package version="3.0" ... prefix="ibooks: http://vocabulary.itunes.apple.com/rdf/ibooks/vocabulary-extensions-1.0/" ...>
nav.xhtml – navigation/semantic file (is needed for EPUB 3 books)
toc.xhtml – Table of Contents in HTML format (you can easy edit style it)
toc.ncx – navigation file (for compatibility with epub2)
The existence of all three files is not a mistake, it just is in the world where the files are to work between epub2/epub3.