The water molecules in the meal absorb the microwave energy when it is heated in a microwave oven. 80–95% of the water in most foods is water weight.
The top few millimeters of pure water readily absorb microwave radiation when it is heated. Leaving the water near and at the surface undisturbed might result in superheating, which can turn liquid water into steam and create eruptions.
Even after the water has been taken out of the oven, particulates in the water have the ability to form bubbles that could pose a risk.
The warning against using microwave radiation to heat pure water is meant to prevent the forceful and uncontrollable vapor bubbles and hot water splashes that can result from overheating the liquid water and can result in severe burns.