Hello Dennis,

in your case switch STP BPDUs and other L2 protocol messages like DTP can be seen as unknown protocols on the router port.

Another example we have seen in our network is that some switches count as unknown protocol drops IS-IS hello packets sent by distribution nodes.

You should be fine.

To check if they are related to STP clear the interface counters and then see the rate of increment if it is one every 2 seconds or N every 2 seconds (if the port is a trunk carrying N vlans) you should have a confirmation they are just STP BPDUs

Hope to help

Giuseppe