If you used shortcodes from a certain plugin or a theme and then stop using either one, then chances are that you still have shortcodes that no longer translate into anything.
Step 1. Install the package
wp package install jaywood/jw-shortcode-scraper
Step 2. run it!
wp jw-shortcode-scraper scrape
To completely remove all shortcodes (active and inactive) from all posts check this simple solution: How To Remove Unused Shortcodes from WordPress