under settings -> table of contents -> processing headings.
make sure your post time is enabled (checked). Whether you are trying to put it on a post or page. Else the plugin will not add the correct html code into the headings.
This is not a solution. One of the most important features of the plug in is that if the user ads more contents(headers) in the page the table of content will update showing the new ones automatically.
This solution does not accomplishes that hence diminishing the value of the plugin.
A better option is simply set the plugin to automatically add table of contents on say 4 or 5 headers in the page, then the user will have to remember to not add more than that number of headers if he doesn’t want to show the TOC on that particular page.
Anyhow, is too bad nobody is maintaining this plugin.
I am reporting the same exact issue.