Hi Gary,
Yes, the current version of the plugin places an index.php file inside the wp-includes folder to prevent directory listing.
We’re in the process of re-implementing this feature such that directory listing is fixed by adding Options -Indexes
to the .htaccess file, rather than creating multiple index.php files.
Can you try to run the WordFence scans, after disabling the ‘Disable WP API JSON’ security fixer within the WP Hardening settings?
Thanks,
Ananda