If the entries aren't appearing in a plain TOC field, that strongly suggests the missing headings aren't formatted in the 'Heading 6' Style.
As for defining the TOC field so as the page #s only appear for heading 6, that's quite possible. Such a field might be coded as:
{TOC \o 1-6 \n 1-2 \h}
This would suppress the numbering for levels 1 & 2.
See also:
https://support.office.com/en-us/art...4-67754d78d05c
http://wordfaqs.ssbarnhill.com/TOCSwitches.htm