Matt Cutts said you should not use it like a "fine-toothed comb" but rather use it like you would use a "machete,"
Hmm. One common issue we see with disavow requests is people going through with a fine-toothed comb when they really need to do something more like a machete on the bad backlinks. For example, often it would help to use the “domain:” operator to disavow all bad backlinks from an entire domain rather than trying to use a scalpel to pick out the individual bad links. That's one reason why we sometimes see it take a while to clean up those old, not-very-good links.
To me this means that webmasters and SEOs are missing too many bad links when they use the tool and possibly often, Google will flag a whole domain as being bad and not just a specific URL. So if you use the disavow link tool too gently, then it might not work. But if you use it too aggressively it might hurt you as well.
Google's John Mueller reshared this on Google+, so clearly we have Matt Cutts saying this, Google's John Mueller sharing it again on Google+. This must come up fairly often.
Forum discussion at Google+.
Image credit to BigStockPhoto for machete man