If I had to choose between thermodynamics and medicine being wrong, and people not being able to accurately estimate how "much" they eat and how "little" they exercise, I'd bet all my money on the latter.
The simple reality is, people have vastly different appetites. I eat fast and am always hungry. I have two coworkers, one eats quite a bit less than me (often struggles to finish a standard portion), the other eats mich more but quite slowly.
3 different people, 3 vastly different eating habits. The reason people gain different amounts of weight most likely isn't in the differences between our bodies, but the differences between our minds.