Personally, I doubt this as the cause. 200 mg of Magnesium isn't a huge dose, and I did look it up in Hale's, and both mag sulfate and mag hydroxide have no reported concerns for baby through your milk (while it does state it causes diarrhea in adults). The frequency of your baby's pooping isn't abnormal for a 3 day old baby, esp. if you milk is in. He may indeed be having some belly pain, though, but this sometimes happens regardless of anything else.
Lots of our clients take Magnesium after birth for relief of uterine cramping and muscles. They normally take a mag citrate or gluconate....something like that.
Mama to ds#1 (7) and a ds#2 (1 1/2)