I don't microwave breast milk because it diminishes the nutrients and I don't microwave ANYTHING in plastic because recent studies have shown that plastic (even BPA-free) can bleed into the food/liquid.
But I do warm up water (almond milk for my own son) in glass and then pour it in the bottle/cup and shake to make sure the heat is evenly distributed. I don't see the problem with using a microwave.
The last time someone gave me a hard time for using the microwave for my son's milk I asked them if they ever ate at McDonald's. They said yes and I asked them how come they were okay with putting fake, processed garbage into their bodies but they weren't okay with using a microwave to heat up liquid. I said "I have never burned [my son] by using the microwave but you, for sure, are putting chemicals into your body". That was the last time I heard about this topic.
