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M$1 Answer
E coli is from contamination from another source. Likely in the factory where they make the cookie dough, but I don't think they have stated the cause of the contamination yet. In the article I cited it states there was possible risk of contamination from E coli.
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M$
The presence of E. coli is an indicator of fecal contamination and poor sanitary practices at some point in the production process.
http://www.cdc.gov/nczved/dfbmd/disease_listing/stec_gi.html#3
However, no contaminated cookie dough has been found so far. The recall was ordered because over 60 people nationwide have been infected with E. coli O157:H7, and all of them reported eating raw Nestle Toll House Cookie dough. There may be other connections between these cases, or no connections at all, but the cookie dough is being recalled as a precaution.
http://www.fda.gov/Food/ResourcesForYou/Consumers/ucm168346.htm