Then you should have seen some warnings/errors on the output in DirectAdmin when you deleted the user, and that would show you what the problem was.
I have seen this happen when I have deleted users wich have a Drupal site, then not all files would be deleted because on a folder Drupal uses 555 permission, and inside that folder Drupal has a file with 444 permission. In those cases DirectAdmin has not been able to delete all the files and folders in public_html, and therfor the user would still remain in the /home folder.
However when this happen, DirectAdmin will let you know about it in the output you get when you deleted the user in DirectAdmin. So it is important to take note of that output. In such cases as I described, you can just log in as root user and delete the user folder manually in shell or sftp from /home/username, because DirectAdmin would already have removed all the other "stuff" exept those remaining files.