I have a CCR (6.41) with no bridges set up. On it I have a port with a vlan configured. On this port when I capture packets I see spanning tree for bridges running with packets going out every 5 seconds it seems. I can't find any way to turn this off? Is it possible to turn it off? If not why not?

Set protocol mode on bridge to none.
https://wiki.mikrotik.com/wiki/Manual:I ... Properties

There is no bridge to set protocol mode on, so I'm not sure how to apply that info.

Sorry for overlooking that previously. Is the router disconnected from any other possible sources of stp packets?

A trick I do once in a while is to do /export verbose, then send it to a file. I can then grep (search) the file to see if there is something I missed. Try that while looking for "stp" maybe...

If you provide a packet trace showing the STP frame with your mac address as the source, plus /export to support they would have to look at it.

Might as well upgrade to 6.41.2 to make sure the problem still exists in current.