It's likely the user showed up in the users list because an attempt and or successful login to Qlik Sense. As you create users in the server's local directory, the easiest way to get them added is to set up a user access rule or login access rule for the userdirectory = to the name of the server.
Alternatively, you can add a user directory connector for the local machine (choose local network) and that should bring the users in when you click the sync button when you uncheck the sync after first login.
Here is a video from the New to Qlik Sense Section you can check out.
Thanks for the responses guys. I had tried the UDC option but that was not working well for me. Turns out the simple solution Serhan suggested works! Simply try signing in with the new user, it fails to let you in because there would be no Token assigned to the user, but it does then place the AD user into the QMC user area. A little tedious when creating many users, but at least it works.