Check the rules on the "Chapter Detection" tab when converting a book:
Code:
[x] Add chapters to table of contents
[_] Don't add links to the table of contents
The first one is associated with the regular expression field, which matches things that contain "chapter|book|appendix" by default when it is checked.
The second includes any links contained in the book into the TOC when it is UNchecked.
Another source of TOC links comes from a book's metadata, such as a LIT book's OPF info.