A Remote Agent can appear stuck in a RUNNING status even though the Agent processes have stopped and the entry in the database also shows a stopped status.
CA Automic Applications Manager
Version: 9.4.x, 9.5.x
This usually occurs after a cloning a database/schema with Agent Running or if a Server is abruptly shutdown without stopping an Agent.
The database entry can be stuck in an incorrect status and sometimes needs to be manually updated.
As the Applications Manager Oracle User, run the below update statements via sqlplus or any other sqlplus client
update so_back_process set so_bp_mesg='Offline' where so_operator='<AGENTNAME>'
Replace AGENTNAME with the actual Agent Name.