Been debugging like crazy the last day with this symptom:
When you run the gpupdate /force command on a hybrid Azure Active Directory (Azure AD)-joined Windows device that’s enrolled in Microsoft Intune, you receive the following warning message:
Updating policy…
Computer Policy update has completed successfully.
The following warnings were encountered during computer policy processing:
Windows failed to apply the MDM Policy settings. MDM Policy settings might have its own log file. Please click on the “More information” link.
User Policy update has completed successfully.For more detailed information, review the event log or run GPRESULT /H GPReport.html from the command line to access information about Group Policy.
Should have Googled it though, because this is “Expected behavior” 
Cause
This issue occurs if the Auto MDM Enrollment with AAD Token Group Policy Object (GPO) is applied to the Windows device. In this case, it tries to enroll the device in MDM when you run the gpupdate /force command. Because the device was already enrolled, you receive the warning message.
This behavior is expected. You can safely ignore the warning message.
Source: Windows failed to apply MDM Policy settings – Intune | Microsoft Docs