Chipotle was rocked this year by reports that more than 60 customers had been infected with e. coli.&nbsp;And yet, Ackman made a bet on the company. On September 6, 2016, he&nbsp;announced a 9.9% stake in the fast-casual Mexican grill,&nbsp;which was purchased at an average price of $405 per share.For its recent fourth quarter, Chipotle's comparable store sales fell 4.8%, with a whopping 14.7% just in December alone. The company's restaurant level operating margins slipped to 13.5% from 19.6% the previous year.While Chipotle's shares have yet to truly tank - they're hovering around $445.45 apiece (and saw a boost of more than 2% Thursday), Ackman wrote down a loss on his investment in the company for 2016.According to his recent letter to clients, the firm took a 0.8% loss on its investment in Chipotle in 2016.&nbsp;It's no Valeant, but it is a risk, with five to 10% of customers vowing to never return to the burrito chain.&nbsp;