First of all E.Coli is not "food poisoning" it is an infection. Next thing is that the fact that it is E.Coli would lead me to suspect that it is possibly meat sourced or produce sourced.There is most likely a failure on two levels. They purchased meat or produce from a poor supplier and they quite possibly under cooked meat or didn't wash their produce properly. Since the outbreak happened at multiple facilities, I would say there is most likely a breakdown in their typical processes. Until authorities are clear how it happened and Chipotle corrects the process and the supplier, I would stay away. All of this is speculation on my part but I spent several years investigating these type of outbreaks.
They had a reputation for "healthy" eating. Now that is totally destroyed. People are just not going to pony up for a E.Coli laden burrito. That many facilities affected means that there is something wrong with the source of their ingredients and their processes.