You can add some pumpkin or yogurt, and that should firm up poops. I'm really bad... I switch my dogs cold turkey between kibbles, when they get kibble meals. But I always add some sort of digestive aid, and I don't have any problems.
I wouldn't worry unless your pup was having persistent diarrhea. Just stick to the 2/3 Canidae and 1/3 TOTW, or even cut back the TOTW a bit, until Indy's tummy has settled.