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I detected a case where I seemed to be able to "miss" commits from the build, though I think I can explain the reason and why the solution requires clearing the workspace.
In my case, I had selected "shallow clone" in the Advanced section and had defined an "excluded region" to include one file. When a commit was made which only modified that file, the plugin correctly did not start the job. That is expected, but because of the "shallow clone", I suspect that the commit was never pulled into the repository at all.
My solution was to delete the workspace, clear the "shallow clone" setting, and perform another build. That brought in the missing commit as far as I can tell.