Prevent branch-indexing triggering builds when a manual build has already picked up changes
I experienced this also. I tried playing with the polling settings in the Multibranch pipeline to see if this could fix it but that only led to no builds being spawned at all in response to SCM changes.
So this behaviour to which you refer was the best of a bad lot.
At time of writing, I think this behaviour is a bug with no current resolution.
Can't remember if I raised a ticket or not as I am in Azure DevOps world now.