If you have a client that is near or over their quota, but their home directory does not seem to match the space usage reported, then they likely have files elswhere on the server.
To find all files on the server owned by that user run the following command.
find / -user $USERNAME > /root/userfiles.txt
Replace $USERNAME with the clients username.
This will search the entire server for all files owned by their username. It will then dump the output into a file called userfiles.txt in the /root folder. This way, you can easily search the file for what you need in your favourite text editor.