For a user to be automatically added to an organization when adding a domain mapping, they must have a verified email address. This occurs when an end-user completes the verification process by following the link in the verification email sent from Zendesk.
If your customer is verified and was still not added, open the user's profile and make a small update to the user. For example, add a space after their name and then remove it. The organization is then added to that user. This is required when an agent or admin manually verifies the end-user's email address.
For more information, see this article: Verifying an end user's email address.