Would not de-frosting puppy food properly give him the runs?

I'm using natural instincts food, the process includes the food coming frozen, and you have to de-frost it, I opened the second packet last night, left it out over night, and ever since we've been using this pack his poo is a lot softer and watery? He is still eating and drinking, so I imagine it isn't that bad. My cats also have food out 24/7 so perhaps he's ate cat food without me knowing? He has been raised on the natural instinct foods even with the breeder.

No defrosting it won't help. Your dog getting into the cats food could make his stool runny. How long has the dog been on the food?

He likely got into the cat food. But also, the pack could have been contaminated with something his body didn't agree with. As worrisome as that is, it does happen. If you continue to feed him the same batch and the loose stool sticks around, trash the pack and get a new one.