My son was milk allergic and when we were doing the tests to try him on cow's milk, the specialist told us to be aware that the transition in "normal" (ie non allergic) babies very often produced a lot of diarrhea, gas, bloating, etc, and that it is normal to take a couple of weeks to get used to it, so for us to not go on those symptoms alone.
If your LO was on regular formula and eating yogurt and other foods containing dairy without problems then it is pretty unlikely that it is not an allergy or intolerance, but you could always chat with his dr...but I do think it is pretty unlikely that it is a problem at this age.