my chicken didn't get hot enough when the rice was done

I tried this recipe, and everything came out great... got a great brown crispiness at the bottom, but I used a meat thermometer and the thickest part of the thigh was only getting to 140F. I feel like the pan never got that hot during the second stage of cooking the chicken. I ended up sticking the chicken in the oven to get it up to 165. Where did I go wrong?