I had trouble with the Artifactory-plugin. I tried to upgrade but kept the issues. Jenkins complained about incompatible configuration and even discarding didn't help. So I decided to remove the plugin. And still the issue above remained.
As mentioned above, apart from the exception everything looks fine. But that data seems to be kept in memory, because a restart removed all the roles.

[Workaround] Find the config.xml and search for unwanted permissions ( permissions related to a plugin you've removed) and remove these. Next restart Jenkins.

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