The Files created through PHP have as user and holder "nobody" instead of the user of your own domain.
Such files are created by default with 777 permissions therefore modifiable by everybody, and can be easily cancelled via ftp.
Some php applications set "umask" (mask of creation permissions of new files) in a different way, with more restrictive permissions, and therefore it is impossible for you to cancel them via ftp.
In order to arrange such files permissions you have to connect to the address:
(replace the domainname.com with your domain)
enter your login and password, once you have entered the control panel click on "Restore correct permissions".
Now it will be possible for you to connect via FTP and cancel the files which you could not cancel before.
We advise you to check the PHP applications which create files because they do not set an umask, and therefore avoid similar problems in the future.