The problem is solved. It was so trivial :D. I unchecked the plugins folder which I added in the preferences. My plugins folder was in the C4D directory, so as you described, it was loaded twice.
Leaning for me: Never place a custom plugins folder in the C4D directory!
Recommendation to the SDK team: Maybe you could adjust the error message in the console, which mentions that plugin folders should not be in the C4D directory. I would assume that many users/ devs will place the folder there, because of a habit from older versions.
Thank you @r_gigante and @zipit for your quick response!