Just an update as I finally got this working. First off this was a lesson of verifying the info giving to you. Come to find out the user had not been enrolled previously. So with that tidbit after much troubleshooting determined it was definitely something up with the user on the Azure side. Working with Microsoft we determined everything was setup for the user in AD, SCCM, O365, AzureAD from what we could see. So what I had to do is actually disable the user and make sure they were removed from O365, AzureAD, SCCM Intune Collection and not showing up in the SCCM db. Then I reenabled the user and verified licenses were correct in O365/AzureAD and showing back up in the SCCM collection and db. It worked. Hope I don't run into this problem too many times but at least I know the work around.