Originally Posted by PatNY
Sigil does not support toc.ncx files. The TOC is destroyed when you open and save an epub in Sigil that contains such a file. I think the developer is planning to add support for it later.
I noticed this. I ran across some epubs that are like the OPs results. I don't see any of the extra entries in calibre's viewer until I open and save the epub with Sigil. I'm not interested enough to figure out why this happens. Most of the time the TOC is not affected by a epub conversion.