Firstly, the qouta doesn't set "home dirs", it sets partitions...
So, if the user saves files in other places that home dir, the quota still applies.
For a list of all files belonging to a specific user, try this command:
ls / -lR | grep (accountname) > name_of_container_file
This creates a text file (name_of_container_file) where the output of the command is stored.
View the file with:
less name_of_container_file
If this file is really empty, then you've probably run into some kind of bug...