Joli Table of contents is set to run last in most environments. It processed “the_content” filter hook at a priority of 10001 by default.

For some reason, if another plugin runs “the_content” filter at a higher priority than 10001, it may compromise the table of contents output. In this case you can set the priority to a higher number to make sure Joli TOC runs last.

add_filter('joli_toc_the_content_filter_priority', function($priority){ 
    return 25000;
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