After we upgraded EM13c, I encountered a problem about automatically promoted listener targets. Since EM12c, I do not add/promote listeners. In earlier versions of EM12c, I had weird problems while monitoring listeners on RAC systems (such as they are detected down although they’re up). Since then, I don’t monitor them (specially SCAN listeners). In EM12c, when I remove a listener, it doesn’t promoted again. With EM13c, I see that listeners are discovered and promoted automatically on each day. First I though, one of my team members accidentally add them, but then I see that it’s an automatic process. After a quick search on MoS, I didn’t find anything and opened a service request. After several mails, Oracle support staff told me that it’s an expected behavior, and I need to disable “autodiscovery” to prevent it (Doc ID 1522674.1) – I really don’t know how I couldn’t find it by myself, but even Oracle support guys spent 3 weeks to find the note 
So if you don’t want your listeners and other clusterware managed targets are discovered and promoted continuesly, you need to disable discovery for these targets:
To disable automatic addition of RAC instance targets:
emctl set property -name oracle.sysman.db.discovery.eventBased.racInstAdd -value false
To disable automatic addition of Listener targets:
emctl set property -name oracle.sysman.db.discovery.eventBased.listenerAdd -value false
To disable automatic addition of ASM instance targets:
emctl set property -name oracle.sysman.db.discovery.eventBased.asmInstAdd -value false
To disable automatic addition of Host targets to Cluster targets:
emctl set property \ -name oracle.sysman.db.discovery.eventBased.hostToClusterAdd -value false
To disable automatic promotion of HAS targets:
emctl set property -name oracle.sysman.db.discovery.eventBased.hasPromote -value false
You need to run these commands on the OMS server (it’s enough to execute them on one of the OMS servers). After you change the property, all the OMS instances must be restarted for the parameters to be active!