Basically, that ebook is a fine example of how not to create an epub. I'd have to see the entire content.opf file to be more certain but it looks as if the manifest section of the content.opf had the toc.ncx file with the wrong type which was corrected but toc.ncx was also included in the spine section of the content.opf which should never happen. In the lines below, the itemref under the spine for ncx should not be there since it would make the toc.ncx displayable.
Code:
<item id="ncx" href="toc.ncx" media-type="application/x-dtbncx+xml"/>
<spine toc="ncx">
<itemref idref="ncx"/>