When creating a domain, you can also set it to have a specified disk space limit (within the limit of your account).
If any of your domains have a limit set within DirectAdmin that may be the cause for that. Using the checkbox to use "same as main account" is advised in most cases.
There can also be a slight delay before DirectAdmin "see" the updated usage statistics.
Another concern is INODES, this is a hard limit, set at 50 000 for free hosting. You are currently using 46 350 inodes. An inode is any file/folder in your account. A common cause of high inode counts is saved emails, one email = one inode.
The only way to increase inodes is to upgrade to a premium account.