Okay. Normally there is a VLAN ID instead of 0, which is missing on the physical switch port. For example: You have created a port group with VLAN ID 10, but VLAN 10 is not configured on the switchports of some uplinks. In this case, the number 10 would be there.
If this is 0, it usually means that you have portgroups where VLAN is set to "none". So the dvSwitch sends the packets from these port groups untagged to the physical switch port. The dvSwitch healthchecks check this, too, but if there is no Native VLAN configured on a trunk port of the physical switch, these frames are dropped and the healthcheck warns about this.
I therefore suspect that the switchport configuration of some uplinks is different. Especially the Native VLAN configuration.