This answer is so simple that you might just be disappointed: the microwaved food may not have been as hot to begin with.
Many factors, such as the type, quantity and thickness of the food affect how it will heat in a microwave oven. If, for example, the container is not right, or the stirring or rotation aren’t thorough, or if the container isn’t covered to keep the steam in, then the heat may not be distributed uniformly throughout the food.
The outer parts may be scalding hot, but the inner parts may still be relatively cool. Then the foods overall temperature will be lower than you think, and it will cool to room temperature faster.
While heating food on the gas the vessel gets uniform heat from the bottom and it slowly rises heating all the molecules in the food. It is important to stir. The temperature of the food heated this way will be even and will take longer to cool off.
There is another reason. Microwave safe containers are deliberately designed not to get hot. Thus food from a microwave oven is in contact with a container that has remained cooler than the food and that saps away some of its heat.