It's fine to use microwave to warm baby's food including milk. Although we may be concerned that the wave could harm food even human body, no scientific research could back it up so far.
Microwave is using the way of 分解食物的分子 to heat up the food, so the food will lose most of the 营养,so no point to warm it by microwave to get food or milk without 营养 for your baby . Maybe it won't bring you any big problem in health (but we never know),but you wasted your food.