What are the potential issues with calling a PHP script in a subdirectory within a WordPress installation?

Potential issues with calling a PHP script in a subdirectory within a WordPress installation include conflicts with WordPress' rewrite rules, which may result in a 404 error when trying to access the script. To solve this issue, you can add a custom rewrite rule to bypass WordPress' default behavior and allow direct access to the PHP script in the subdirectory.

function custom_rewrite_rule() {
    add_rewrite_rule('^subdirectory/([^/]+)/?$', 'index.php?pagename=subdirectory&custom_var=$matches[1]', 'top');
}
add_action('init', 'custom_rewrite_rule');