Coccidia can be a problem for young puppies (many older dogs also carry it, but have no/few symptoms, as their immune systems are more mature). But I assume your vet has already checked for this. It must be treated with special medicine and is difficult to clean from the environment.
Feeding too much at one time (especially some of the high protein kibbles) can cause diarrhea. My dogs also have had difficulty with foods containing chicken and fish, and also grains (rice has been ok).
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