Sigil uses heading tags to make TOC entries. If your file doesn't have heading tags, Sigil can't make TOC entries. But calibre usually makes TOC entries from heading tags too, so I don't see why your file is being problematic.
As AnemicOak noted, you will have to wrap them in heading tags to make it work.
It is necessary for Sigil to regenerate the TOC since the XHTML files are concatenated, manipulated and cleaned during import, so the original NCX doesn't have much sense anymore.