Is she suggesting that putting water into the microwave creates some new chemical compound that isn’t H2O?

Maybe it's the new compound called radiolytic compounds microwaves produce that are not found in humans nor nature according to Dr. Mercola.

Structures of the water molecules are torn apart and forcefully deformed. This is different than conventional heating of food, whereby heat is transferred convectionally from the outside, inward. Microwave cooking begins within the molecules where water is present.
Contrary to popular belief, microwaved foods don't cook "from the inside out." When thicker foods are cooked, microwaves heat the outer layers, and the inner layers are cooked mostly by the conduction of heat from the hot outer layers, inward.
Since not all areas contain the same amount of water, the heating is uneven.
Additionally, microwaving creates new compounds that are not found in humans or in nature, called radiolytic compounds. We don't yet know what these compounds are doing to your body.

Lol. Seriously, if you are bored and need a laugh, I recommend giving it a read.