Microwaving breastmilk, or heating it on the stove, can cause a loss of Vitamin C content, along with loss of some of the milk's special anti-infective properties. The higher the temperature, the more pronounced the effect. (Quan R, Yang C, Rubenstein S, et al: Effects of microwave radiation on anti-infective factors in human milk,Pediatrics 89:667, 1992; Sigman M, et al: Effects of microwaving human milk: changes in IgA content and bacterial count, J Am Diet Assoc 89:690-92,1989)
It's important to remember that uneven heat distribution, from microwave warming, resulting in "hot spots" can be hazardous. The center of the fluid may be much hotter and the milk may scald your or your baby.
You do bring up an interesting point. Though parents are told not to microwave breastmilk for several reasons, we often forget to mention that heating milk on the stove can also be problematic.