Our puppy came to us with horrible digestive issues. She was underweight and vomiting daily. In addition to following a deworming protocol from our vet (which never produced any visible parasites) we put her on plain boiled boneless skinless chicken breast for a day and then slowly began incorporating Nutro Ultra Puppy kibble with a splash of filtered water over a few days until she had transitioned completely.
She now eats Nutro Ultra Puppy (large breed) kibble for all three meals a day, still with a splash of filtered water.
I've had excellent results with this food, with multiple dogs. Very firm, well-formed poops.
I also feed Peggy daily frozen "treats" of a green bean or two, a baby carrot, or a slice of banana. And I plan to freeze teaspoons of puréed pumpkin soon, and add them to the rotation.
One good option if you're happy with the food you're feeding your pups, and have ruled out any serious illness or parasite, is to eliminate all treats and then reintroduce slowly, giving each one a few days to produce symptoms.
My last dog had horrible diarrhea as a pup, which even had blood in it once, and I ultimately traced it to freeze-dried liver treats. My vet at the time offered ZERO help with this. I had to figure it out on my own.