That happened with my son. He always wore Huggies since he was newborn and then to try and save a little we bought pampers instead once. We noticed he started having a rash all over his stomach and back and figured it was diapers. So we switched back to Huggies and the rash went away so that could possibly be your babies problem.
if they started coming when u started giving him formula is the formula just don't give him any milk put him on pedialite for 24 hours so is stomach can clean the milk out and then try soy milk formula