Chipotle's sales are down because even their most loyal customers were staying away in the fourth quarter of 2015. I'm sure some loyal customers got sick from their food in 2015, like the 234 confirmed cases in Simi Valley, CA in August.
Let's break down these numbers: it was estimated that 3,000 entrees were sold during a two-day period. Let's say each entree was sold to an individual person, and that the number of cases was under-reported by half -- that would mean 500 out of 3,000 people got sick. Therefore, 83% of people who ate at a Chipotle location that had "failures in pest control, sanitation, and maintenance" were fine. Sounds like a description of my last New York City apartment.