I'd installed a Cloud Control 12c, when deploying agents to the hosts which have 6 databases on it, the discovery process only found 2 of them. I went to Setup - Add Target - Auto Discovery Results.
See 'Understanding Database Discovery in Enterprise Manager 12c Cloud Control (Doc ID 1400463.1)'. on MOS.
Section 'Has the database been discovered?".
Thanks Dave, that note helped me a lot.
Does filesystem permissions needs to be changed on the respective ORACLE_HOME to allow 12c agent user view something? I mean, Do the OH needs to be changed to 755? Or perhaps the agent OS user needs to be part of the dba OS group?
How you accomplish it is up to you but I believe the proper method is to use group access.
See Installing Oracle Management Agent section "Installing User Requirements"