I would suggest using lsof and look for files marked as (deleted). It is possible that a process still has a file open that has been deleted from the filesystem. In this case, the space will not be reclaimed until the process closes the file. You can force this to happen by killing the process, but this should be a last resort option.
First - reboot the server
Then go under each directory under /, like /var is a good start and run "du - sh ./" command. You may see abnormalities. Check the size of the log file /etc/httpd/logs
see /var/log files (ls -lh)
see files under /var/www/html
these are the places where usually files are growing. Otherwise you server may be hacked and somebody is putting files anywhere they want.
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