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Ah, I see. Yes, the reason is that you also run CheckStyle. For all of my plugins I'm checking if there is already a result present. If there is one there then I'm skipping the step. You can check this by running the goals in the opposite order: mvn scalastyle:check checkstyle:checkstyle. Then you will get Scala warnings but no Java warnings.
That means I need to run the checkstyle reporter multiple times. I.e. in the end there will be multiple Checkstyle results available for a build.