The section levels that appear in your Table of Contents are set according to your book Theme.
Here is the setting for the Nonfiction book Theme:
Here is the setting for the Technical book Theme:
Here is the setting for the Fiction book Theme:
And finally, here are the options available in the Custom book Theme:
To get sub-sections to show up in your book's Table of Contents, select a "Custom" book theme, choose "Parts, Chapters, Sections and Subsections" in the Table of Contents section, and then scroll to the bottom of the page and click the Update Theme button.
Please note that Custom book Themes are part of Standard and Pro plans. Here is an article about our Book Themes: http://help.leanpub.com/en/articles/3691789-what-are-the-settings-for-each-of-the-different-book-themes.
Your plan can be edited at https://leanpub.com/author_dashboard/subscriptions.
For more information about how the Table of Contents, works in Leanpub books, please see this article.