An EPUB 3 navigation document is to allowed to be part of the spine of the book. From the EPUB 3 spec:
Quote:
Note that the navigation document is not exclusively for machine processing. Formulating the document as an XHTML Content Document enables its reuse in the linear reading order of an EPUB Publication, avoiding the creation of additional tables of contents (i.e., it can also be added to the spine [Publications301] ).
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I suspect the problem has to do with Sigil or your use of it.