I'm just learning SIGIL so I encountered that issue as well.
You have to go to the tools/table of contents/generate table of contents interface.
And there you have to uncheck the "show TOC ....only" box and it will give you an overview of what's been checked and what hasn't. This should give you an idea of what you need to uncheck to clean up your mess.
It takes a while to figure out what's going on with SIGIL. Like most programs, it has a mind of its own.

I've been at it for 12 days. Getting used to it.
Also, I only use H1 headings for my TOC. If you were to add subheadings, I would go with H2. In that way, you can also use the select menu to focus only on those two types of tags. Again, you have to get used to looking at SIGIL and what it's trying to do.
This is based on my experience. Hence, it's not SIGIL law.