We use AD too and synchronise the users with the AD on a daily basis. When a user gets added to the server they need to be given a site role. Depending on how you 'import' your usrs will depend how you set the site role. If one isn't set then they will possibly appear as Unlicensed.
The site roles are discussed here - http://onlinehelp.tableau.com/v10.1/server/en-us/users_site_roles.htm
We personally use the inbuilt AD Sync functionality of Tableau Server and all our users are added with the minimum site role of 'Publisher'. We changed this, but I can't recall what the default was.
I see users get set to Unlicensed when they have left the company and their AD account no longer exists. I just remove them manually via the Server UI.
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I have seen this when the users own content on Tableau Server....Tableau won't allow you to remove an user without first changing the owner of the content (Workbook, Project, etc...)
Yes Nick! Thanks a lot for the info.