Hi Jenny
Indeed there are a few reasons this may happen.
First, simply excluding a topic or a book in the TOC simply makes sure that the TOC doesn't have a link pointing to the topic. Normally, I'll just tag the topic itself and ignore tagging the TOC. If a topic has been excluded, it won't appear in the TOC.
In the WebHelp SSL recipe, click to expand the Content Categories section and look at the settings on the right. You might try ensuring the following option is enabled. It's named Exclude Unreferenced Topics from Output. As long as nothing else is linking to the topic, ensuring it is removed from the TOC *SHOULD* cause it to no longer be included.
Cheers... Rick