I recently had the same issue. After looking into I found out that my SNMPv3 encryption method was recently changed on the node I was monitoring but was not changed within NPM. The only was I was able to get rid of those unmanaged interfaces from NTA was to re-add the node with the correct SNMP settings. Without SNMP, NPM can't get the actual name of the interface and when NTA receives traffic from an "unknown interface" it seems to assign it a random number from what I have noticed. I may be wrong about the whole random interface number but what I have above fixed my issues with said case.
Ours got fixed after the device was rebooted...I know its not always possible but, it is what worked after looking into the issue for a few months