If you are experiencing 404 errors in non-wordpress sub-directories you can fix in most instances by adding “ErrorDocument 401 default” to your WordPress .htaccess file.
In most cases a 404 error will not happen when accessing non-wordpress sub-directories unless they are secured using htaccess password protected directories or a script that will generate a 401 Unauthorized error.
When using htaccess to protect a directory for example, a 401 Unauthorized error is thrown until the proper credentials are entered. By adding the “Error Document 401 default” the web server will find a default page and not throw a “404 Page Not Found” error as we have now set a default page for 401 errors.