The navigation ToC (on the Kindle, the GoTo menu) is independent of the html ToC (an actual page in the book, containing hyperlinks). You can have one without the other.
Sigil and calibre editor both have a handy ToC editor, if you need to touch up your book.
Add a link to the titlepage to make them happy.
I wonder about that error, though. An EPUB doesn't require a specific number of ToC elements.
Edit: darryl, you got it in one.