Hello,
From AIQ Config Advisor release notes it appears that FlexArray is supported (there are known issues with FlexArray listed on it - version 5.8 page 9).
Firstly I would suggest that you check that zoning alerts. Please refer to the Fabric-attached MetroCluster® Installation and Configuration Guide to understand which ports should pertain to which zones. Then check at least one of the warnings against that recommended configuration.
But, If you are 100% sure no one changed any MCC config since deployment, and that in the past your ConfigAdvisor runs never showed an error like this, I recommend that you open a ticket. https://track.netapp.com/Ticket/config-advisor/30
Regards,
Pedro Rocha.