I assume this is the Virtualmin dashboard that you refer to above: then the additional files taking up all the extra space are somewhere inside the /home/website directory.
Run the following as root from that directory:
list of files 50 Megabytes and larger
find / -type f -size +50M -exec du -h {} ; | sort -n
directory using most inodes
find / -xdev -printf ‘%h\n’ | sort | uniq -c | sort -k 1 -n