If previously disk quotas were disabled on a Directadmin server at the system level, i.e. partitions were mounted without quotas. And once you enabled disk quotas and if there are already Users created in DA, then you'll also want to reset their quota limits.
Run the following commands:
cd /usr/local/directadmin echo "action=rewrite&value=quota" >> data/task.queue; ./dataskq d2000
to ensure an upper disk usage limits are enforced.