There are no entries logged for this warning in the Event logs.
A Dtrace if the MMC process will show the following:
(mmc) <14160> EV:L {VaultCreateInstanceRequest::CreateInstance} CLSID [{F4D3EB5B-C7C5-11D1-90DB-0000F879BE6A} (EnterpriseVault.DirectoryService.1)] Server Name [localhost] Used Server Name [localhost] Num of attempts [1] Total elapsed [0.003s] Result [Success (0)]
(mmc) <14160> EV:L {CBaseDirectoryServiceWrapper::CreateAndPopulateVaultObjectEx} Number of records [1]
(mmc) <14160> EV:H {CImportPfxCertificate::CheckIfCertificateValidForServer:#220} caught exception [0x80004005] [Unspecified error ]
After clicking on Import, Figure 02 below shows an example of the certificate having the Host FQDN in the Subject (Issue to: evvirtual1.kvs.local), and the alias FQDN (evserver1.kvs.local) can be found under the Alternate Names
Figure 02 - Certificate details

After Clicking on OK, a Warning is shown stating that the EV Alias evserver1.kvs.local was not in the Certificate as shown in Figure 03 below
Figure 03 - Warning Message

JIRA: CFT-3794