The report doesn't really say how this happens or what it means exactly. Does this result from say, people's fingers getting cut by the processing machines and little bits of flesh going in, or is it human waste ending up in the mix somehow?
"It's really easy to contaminate PCR reactions with human DNA, on account of the technicians being human and thoughtlessly shedding DNA at all times. You can prevent it, of course, but most labs that usually deal with non-human taxa only don't bother to, because it doesn't matter and it's a tremendous hassle and significant expense to do so. Unless this was done in a forensics lab, that would be my guess as to the source of the human DNA in the reactions."
http://www.metafilter.com/154105/Quality-meat-No-fillers-Or-...
They do say, "While some of these substitutions, hygienic issues, other variances, or off-label ingredients may be permitted by the FDA, our scientific disclosure allows you, as the consumer, to decide whether the variance or problems meet your personal standard in your buying decision."
Some of these problems like pork in pork-free products or having 10g protein as opposed to 25g seem to be big problems that need some sort of investigative follow-up like contacting the companies for a statement about the findings.
This implies it's not as common as you suggest.
>2/3 of the human DNA samples were [in] vegetarian products. >10% of Vegetarian products contained meat.
Sounds to me like the meat hotdogs are the better ones.
Also, if the human DNA was caused by sample contamination in the lab, it could just be that the contamination is more likely to be detected in a vegetarian sausage than in a meat one.