Under certain circumstances User Profiles are not written back to the UPM User Store during log off. 

Recovery Step: 
Rename or Delete these profiles in the user store and let UPM create a new profile. 

Preventative Step: 
Introduced in Profile Management 5.5, Profile protection provides profile protection by enhancing the way Profile management handles profiles. Profile management maintains a last known good backup of the NTUSER.DAT file. If Profile management detects corruption, it uses the last known good backup copy to recover the profile. For more information, see Profile Management\Registry.

If your environment is prone to this behaviour, enabling Profile protection will prevent the corrupted local Registry from overwriting a good Registry on the User store and limit the chances for this issue to occur. 

Problem Cause

During an earlier session, the user Registry may have become corrupted and was written back to the user store.
As the profile is recognised as corrupted during logon, these profiles are not considered UPM profiles when users log off and stay on the local server upon users' logoff. 
In the Profile Management log, searching for the word "corrupted" will indicate that the profile is deemed as corrupted and may encounter the issue. 

2015-12-16;09:19:49.131;ERROR;[DOMAIN NAME];c0002064;25;28092;ProcessLogon: Copying the user's registry hive failed with: The file or directory is corrupted and unreadable.

2015-12-16;09:19:49.131;ERROR;[DOMAIN NAME];c0002064;25;28092;ProcessLogon: Copying the user's registry hive failed with: The file or directory is corrupted and unreadable.