After upgrading to Matrix Authorization Strategy Plugin 3.0 (and some other plugins) we noticed that all existing multibranch branch jobs (possible PR jobs are affected as well, we didn't have any though) are listed as "Ambiguous Permission Assignments". When investigating we see that they all have permissions for SYSTEM which is flagged. But as the branch (and PR) jobs for a multibranch pipeline are created automatically there is no way to migrate this permission. Se attached image.
Checking the config.xml file for such a branch job I see the following config:

    <hudson.security.AuthorizationMatrixProperty>
      <inheritanceStrategy class="org.jenkinsci.plugins.matrixauth.inheritance.InheritParentStrategy"/>
      <permission>hudson.model.Item.Build:SYSTEM</permission>
      <permission>hudson.model.Item.Configure:SYSTEM</permission>
      <permission>hudson.model.Item.Delete:SYSTEM</permission>
      <permission>hudson.model.Item.Read:SYSTEM</permission>
      <permission>hudson.model.Item.Workspace:SYSTEM</permission>
    </hudson.security.AuthorizationMatrixProperty>