I clearly should have written a better bug report, because I can't reproduce the exact point ;-)
This is about the functions 'error' and 'exception' in https://github.com/wikimedia/pywikibot-core/blob/master/pywikibot/logging.py.
def output documents the meaning of the various parameters, but all of the other logging functions (def error, but also e.g. def warning, which was not mentioned in the bug title) are missing the extended documentation. That documentation should be added.