Hi,
look at the other end of the line. The port on the neighbor switch probably belongs to other VLAN.
Cisco devices are seeing which VLAN the other end of the lines belong via CDP protocol. Is there is a mismatch they report Native VLAN mismatch error even in the case there is no trunk defined.
You should see similar message in the syslog, too.
If you want to persist on the current VLAN membership just
set logging level cdp 3 default
on CatOS switch and these syslog error messages will stop.
But CiscoWorks will still report logical discrepancy.
Regards,
Milan