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There's a whooopoooole lot of factors that can be involved, and it can be a combination of all of them.

Background: microwaves don't just heat water, they heat things with molecules that, like water, have a lopsided electric charge. When the microwave energy comes in contact with something, it either goes through it without interacting, bounces off of it, or is absorbed. Light with a window, a mirror and black paint is the same.
Lopsided molecules absorb the microwave and wiggle, and wiggly molecules are what we perceive as hot.
Microwave safe items are transparent to the microwave energy, and it goes through to the food.

Depending on the material your plate or bowl is made of, it might not be properly microwave safe. Some ceramics have the lopsided molecules microwaves like, so they get hot.
The bowl might also be made of a material that transfers heat really well. Think about how air from a hot oven is tolerable to have hit your face but significantly colder water is lethal.
It's in continuous contact with something that's getting up to boiling, the steam on the food, and so it gets hot quickly and transfers the heat to your hand easily. Since water can absorb a ton of energy before turning to steam, the energy is there for a while and there's plenty to heat the bowl.
Finally, microwaves have hotspots, even with the rotating tray. This can work with either of the previous two things to allow the food to stay cold while pumping a lot of energy into the bowl or one spot in the food. It's why a lot of reheat functions run the microwave and then sit for a few minutes:it lets the heat from the hotspots even out.