I see where you are coming from, rfc1180..
We can look at 2 different scenarios, the first being a trunk port -to-trunk port connection between two different switches with 2 different native vlan id's as depicted in the link. This can result in the PVID inconsistency situation.
Scenario 2 which I am referring to is an Access port assigned to a VLAN, connected to a switch with no vlans configured, or vlan1 as native. Both switches have native vlan1, but with switch#2 is connected to a VLAN access port that expects vlan tagged packets but switch#2 doesn't tag vlan1 there is a mismatch. Switch1 says I'm getting pbdus on a port where I should be seeing tagged packets, so the native vlan on connected switch must be incorrect. Since I'm not trunking, then I have no visibility to the other switches VLAN's, nor do I care. We use this technique all the time when we use VLAN's on a core switch to segregate tenants in a building and allow the tenants to connect whatever kind of switch they want to the port we hand them.
I would be curious to know if the ports are becoming error-disabled out. A reboot would clear this condition until it happens again over time.
@omar_nagy - can you check the status of "show interface | include disable" before you reboot the switches?
A negative return on that command will mean they are not erroring out. Else it will return a list of ports in error-disabled condition.
If they are, indeed error-disabling then we can put some conditions in that will allow it to correct itself so you don't have to reboot it every week.
