It will not do that unless there is an inline TOC in the book. The true ePub TOC is a separate file that is not in the book at all. Calibre has been known to place the TOC at the end of a mobi book. Did you generate a mobi file using Calibre and then convert it to ePub?
The fix is to find the inline TOC at the end of the book and simply remove it. It will likely be the last file in the list of files.