My Autosupport builds the recommendation once when the ASUP arrives, there is a chance that partner's asup is not yet processed causing this warning. This doesnt cause the controller and neither the internal PSDB recommendation thats seen in internal tool.
If you're taking about the system warning LED on the physical controller, that typically indicates a hardware component failure/degradation. It would not be related to this "sam.misconfig" warning in HealthCheck.
I would examine the environment, storage and EMS/messages files for evidence of a hardware problem. If it's not obvious, open up a case with NetApp Tech Support.