I recently noticed that I have missing pages in the TOC. I am not sure what is going on. I have deleted those pages from the TOC and then created and linked them again several times by different ways. I republished and cleared my cache, but still not resolved. I have also notice I can't search my project containing that information either when published to the web, but if I have a direct link I can see the information. If anyone has feedback that would be greatly appreciated.
Check the condition tags on the topic and in your output setup. Often when you add something to the toc and can't see it, it's because of the conditions on your topic being excluded by the output build expression.