Numbered Headings is compatible with the Table of Contents macro and the numbering added through the app is used in the table of contents.
The Table of Contents macro scans the headings on the current Confluence page to create a table of contents based on those headings. This helps readers find their way around lengthy pages, by summarizing the content structure and providing links to headings.
The Table of Contents macro has several options. One of the options is to enable the Display Section Numbering option. When you use Numbered Headings on the page, you must make sure to disable Display Section Numbering to prevent double numbering.