I agree with Timesheet. Trying to get the "bad" links removed is likely to be an exercise in frustration. In many cases, you'll have no way of contacting the sites concerned. And, if you do contact them, chances are that most of them won't take any notice of your request.
Nobody knows this for sure, but I strongly suspect that we worry too much about these supposed bad links. Despite what we've been reading recently, I can't imagine Google downgrading a site merely because of something that is outside the site's control. It would be different if you had entered into a reciprocal link arrangement with these sites, or if you were seen to be promoting them in some way, but I assume that's not the case here.
Better to put your efforts into getting high-quality links - and, of course, in developing the best possible content, so that other sites will want to link to you in the first place.