Example of the diff is here.
The bot correctly identified that ref name="medium 2012" is being used twice in the article.
Unfortunately, references could be defined not only in the article itself, but in the final reference template. I personally don't like putting all references in the end but, as I checked, the same behaviour exists not only in ru.wiki, but en.wiki, too.
I suggest adding an additional check, whether <ref></ref> is inside of template or not and fixing the reference that is outside of the template.