My 2 best guesses is bad sanitation, or keeping certain product (like at the prep station) too long at room temperature. And you can google any restaurant name + food poisoning, and it's rarely the result of the Chain itself. Rarely you'll get something like tainted product, but usually it's the local employees at a location fucking something up that causes people to get sick (like your friend's sister). I wouldn't blame you at all for not going to that location yourself, but it's a real stretch to come to the conclusion that all of Chipotle's food is terrible and makes people sick just because people got sick eating at a particular location.Any place that just leaves food sitting in the hot plate for hours at a time is bad news. If it's not being cooked for order, it's shit.
You friend's sister potentially being part of the problem is just extra lulzy.