This behavior can occur if the Management Pack for Active Directory is installed and if the domain controllers in question do not have the Operations Manager client agent installed. Active Directory Topology Discovery tries to discover all domain controllers regardless of whether the agent is installed.
For complete details as well as a resolution, please see the following:
KB3068465 - Domain controllers are unavailable in the Operations Manager console when no client agent is installed ( https://support.microsoft.com/en-us/kb/3068465 )
J.C. Hornbeck | Solution Asset PM | Microsoft GBS Management and Security Division
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ConfigMgr 2012 R2