The nature of disk space quotas ensures that accounts can not use more than their assigned quota. Thus, if an account reaches it's quota limit, additional files can not create, and services such as email may fail. You can browse to the "Notifications" tab in "WHM Home » Server Configuration » Tweak Settings" to ensure email notices are sent out when an account reaches it's disk space quota.
Is it possible the quota of that account was modified after the usage, or that the usage occurred at a time when the quota was not enforced? Is the user able to upload new files to the account?
The account should receive an error message when uploading new files if quotas are active on the server and the account is at it's limit. Please open a support ticket for this issue using the link in my signature so we can take a closer look. You can post the ticket number here so we can update this thread with the outcome.