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I was recently asked to update the EBS Plugin from 12.1.0.2.0 to 12.1.0.3.0 in my Cloud Control 12 setup. During the prereq steps I got an error: "EM-04050: The selected plug-ins cannot be deployed on the Management Server because there are some Management Agents on which incompatible versions of these plug-ins have been deployed."
Unfortunately no other information was given. I knew there must be some old versions of the Agent plugin floating around out there but didn't have an easy way to find them. Oracle Support to the rescue... Run the following against your SYSMAN schema:

select t.target_name||' - '||plugin_id||' - '||version||' - '||rev_version||' - ' || plugin_bits_type 
from em_current_deployed_plugin cdp, mgmt_targets t, em_plugin_version pv 
where dest_id = t.target_guid 
and pv.plugin_version_id = cdp.plugin_version_id 
and target_type = 'oracle_emd' 
and plugin_id='oracle.apps.ebs' 
and version='12.1.0.1.0'
order by deployed_date ;

You can use this for any other plugin byt changing the "plugin_id" to the ID the plugin you are interested in checking and version to desired version.
After running this I was able to find out exactly which agents were using the old plugin and needed to be upgraded or deinstalled.