Google has always shown links in WMT as well as the output of their LINK: operator that likely have zero influence on rankings. They often include NOFOLLOW links as well as links from URLs known to be under penalty. Both WMT and the LINK: operator display a sample of links known to Google, but that's about as much as you can infer from their existence in either place.
Just because they appear in WMT doesn't mean they "count". It's just another way that they keep webmasters/SEO guessing so they can't reverse engineer link related portions of their algo.