Usually the problem is not a question of which script creates them versus which script deletes them, but a matter of which user the various scripts are running as.

A server like Apache typically uses "nobody", so any files created by a script should be deletable by a similar script on the same site. Things get tricky if you're trying to mix with an FTP daemon that might be using, for example, the user "ftp" instead. There's also the possiblity that the Web server is using some kind of "SUID" CGI mechanism to assign each site its own user.

That's when permissions on the files are very important. You might want to check with stat to see who owns them, and if you're able to write to the directory they are in, which is sometimes required to effect a deletion.

If you can get in via shell, you can use the long directory listing (ls -l) to see who owns what.