Yea this is blatantly false. I worked at a processing facility for a few months between my last semester at college that provided all of the beef for our local Chipotle's. All that shit is sent to them raw, they cook on site.Its all cooked and prepared off site, bagged, and brought in, whereas other burrito places still cook shit in house.
So that's almost certainly related to it, though investigation wise, no one has been able to come up with what exact component or practice in Chipotle's supply chain has led to the food poisoning epidemic, but its has definitely hurt their business. Hence why they're giving away free burritos.
The issues with E-coli have stemmed from their produce if I recall correctly meaning the problem either lies with the produce not being processed correctly before being sent to Chipotle (farms not following regulations on the amount of time prior to sale that manure can be used), Chipotle not checking the produce and washing it prior to using it in their lines, or employees rubbing shit inside your burrito.
If I misread that and they haven't determined where the E-coli is coming from then fuck, I am at a loss.