Sorry to bring up this old thread but I am seeing a similar thing on WMT. To cut a long story short I have moved from the www to non-www version of my website. I did this because of a large number of 'inorganic' links pointing to my website that, despite my best efforts, I just couldn't get removed.
I have seen a number of links listed on WMT with 'via this intermediate link'. The thing is, the www version of my site (where the links point) is a dead end as it simply doesn't exist any more. I don't have any preferred domain set in WMT and there is no redirection between the pages/sites.
I don't know if these links are actually counting as 'votes' for the non-www version of the site or whether they are being listed (perhaps temporarily) so that I can see they exist and request that they are pointed to the new location if I feel it would be valuable. I can only see what I would deem to be 'good' and 'organic' links actually being listed in this fashion at this point but I don't know if the picture is complete.