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Hello @mommaroodle,
Thank you for contacting the support.
The shortcodes are rendered in the front end and our plugin runs the tests on the content present in the post editor in the backend and that’s why the headings added using the shortcodes will not be recognized. If you want our plugin to read the data from the shortcodes, you will have to get in touch with the developers of the plugin you are using to generate the shortcodes and ask them to integrate our content analysis API into their plugin so our plugin can read the data correctly. You can share the following guide with them: https://rankmath.com/kb/content-analysis-api/
Hope that helps. Let us know if you need any other assistance.