Question about disk usage calculaton

OS type and version Almalinux 8.5
Virtualmin version 6.17

I have a VPS with single user, I set the disk quota limit on 25GB.
DU command (or ncdu) shows that user only use 5GB
database disk usage using ncdu command shows that /var/lib/mysql use 1GB.

That means I can assume that user should only use 6GB. But it is showing over quota and unable to renew letsencrypt cert.

Now after I make it unlimited quota, it shows 22GB usage. How can I trace what is consuming disk quota for that user?

See Email is full? Or the User is full?

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