Last day a few domains started throwing incorrect disk usage in WHM. The accounts has a lot of files, but the disk usage was reported as 0 in List Accounts section. Upon checking noticed that someone had played with the fstab and /home was not mounted with usrquota correctly. Did the following to correct it.
Alternatively, you can reboot the machine, so that the changes will be picked up from the fstab after making changes.
When it is executed, make sure /home is mentioned in the output. After the successful completion of its execution, relogin to WHM-> List Accounts and check the disk usage. It should be corrected.