You should be able to see the mismatches in the Health Status Details (see e.g. ESXi 5.1 Network Health Check VLANs)
André
I ran into this today along with an MTU message. I went to the list of hosts assigned to the port group causing the problem and found that the ONLY GREEN ONE was the issue in that it had a 2-port card down. After putting it in MM and rebooting it, the alerts on all the other hosts cleared immediately. Hope that helps.