On TechNet, Microsoft provides a list of Know Issues with Virtual Machine Manager in Release Notes for Virtual Machine Manager in System Center 2012 R2. If you have trouble or bugs in System Center 2012 R2 Virtual Machine Manager you should definitely check out that page. Here is a short list from 20.01.2014:

  • File servers under management will go into an unknown state after upgrade
  • VMs with shared VHDXs are displayed as “Incomplete VM Configuration”
  • File Server VM migration fails from an MSU host, resulting in Incomplete state
  • A VM on a VMware ESX host cannot be assigned to a cloud while it is running
  • Windows Server Gateway: all gateway virtual machines on a given host cluster must use same back-end network
  • Cannot manage Spaces storage for Scale-out file servers on Windows Server 2012
  • Operations Manager Health Service Might Restart Creating Inaccurate Chargeback Metrics
  • Cannot enter or change application and SQL Server settings directly in VM templates
  • Cannot manage Spaces storage for Scale-out file servers on Windows Server 2012
  • Disk classifications not displayed correctly after a new LUN has been registered
  • VMM no longer supports VDS Hardware ProvidersVMM cannot manage General Use file servers on Windows Server 2012 R2
  • VMM does not manage Storage Tiering in Windows Server 2012 R2
  • VMM does not manage Write-back cache in Windows Server 2012 R2
  • File Server Tasks Not Supported on Untrusted Nodes
  • Incorrect Server Error Code Returned for Invalid Library Paths
  • Windows Azure Hyper-V Recovery Manager Does Not Accept Replication Frequency Changes
  • VMM does Not Provide Centralized Management of WWN Pools
  • Windows Server Operating System MP Disabled by Default
  • Service deployment fails and the guest agent on virtual machines does not work as expected
  • Management of VMs deployed directly on NPIV-exposed LUNs is not supported
  • Windows PowerShell help might not open as expected on computers running
  • Deploying virtual machines to hosts on perimeter networks might fail
  • Registering a storage file share on a library server might cause an error
  • Failing over and migrating a replicated virtual machine on a cluster node might result in an unstable configuration
  • Modifying Tenant Administrator permissions affects permissions for self-service user roles
  • Member-level permissions for network quotas are not applied for the Tenant Administrator role
  • Canceling and restarting when creating a new virtual machine might fail
  • BlogEngine service deployment fails

Check out the TechNet article for workaround or answers.