When chipotle first started the lines where long and the food was good. Their process flow was optimized for the constant stream of customers.
They had a large staff of people for the size of the restaurant so people had dedicated jobs with a few who spent all day cleaning.
They were always way under on their holding times for the food. They separated people handling hot and cold ingredients and the till.
From a foodborne pathogen aspect it was a really safe place to eat.
Then they overbuilt, increased their prices and lost quality control. Their customer flow started declining. With the decrease in customers, food was pushing holding times, crews were reduced so more cross-contamination occured, and cleaning fell way behind.
Today Chipotle can be referred to as “shitpotle” as the probability of foodborne disease is pretty much guaranteed.