User Device Tracker and Network Performance Monitor match on the Interface Index. The interface Indexes could have changed between adding the Interface in NPM and adding it in UDT.
I have checked random interfaces on my Instance, and it does go to the correct Interfaces.
To globally enable ifindex values that are maintained across reboots, issue the snmp-server ifindex persist command in global configuration mode. The same command can be issued to enable ifIndex persistence only on a specific interface in the interface configuration mode.
I removed and re-added the device and it still came up with the same error, although this time it was mis-matched to different ports.
It's a juniper device. What's strange is that by default in NPM it has a number of alias ports, as well as the physical ports. Quite often it's one of these alias ports that UDT will link the port to incorrectly.
I removed and re-added the device and only selected the ports in NPM that UDT could see. This seems to have fixed the issue.