WP All-In-One Security “Advanced Character String Filter” setting causing htaccess rules for sub-directories to not work

The All-In-One WP Security plugin has a setting under Firewall > Additional Firewall Rules that can create rules in the .htaccess file that will prevent some sub-directories to stop working resulting in a 404 error. The setting that is causing this is the “Advanced Character String Filter”. Disabling this setting has fixed the issue on a WP site that was using ShopSite.