Backdoor in Cpanel for addon domain names

Finding index.php and other files in the webhosting server, when login using FTP and File manager, However when the url is checked in the browser the files are not loading, the default index.php is being displayed.
was facing the problem with one webhosting company, now facing the problem with another webhosting company.
Does anyone know of any backdoor with Cpanel.
For non cpanel webhosting the problem is not faced.