To resolve this issue, update to Server app v2.2.1 or later.
OS X Server: Unable to import an intermediate and leaf certificate in Server app
If your Certificate Authority sends you both an intermediate and a leaf certificate in response to your Certificate Signing Request, an alert may appear in Server app v2.2 when attempting to import the certs if the intermediate cert is not already in your keychain:
"An error occurred on the server while processing a command.
The error occurred while processing a command of type 'importCertificates' in plug-in 'servermgr_certs'."
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