Well some of the food we eat generates flatulence of which 7% can be methane. Meaning this leaves our system without burning. As such in calorimeter it would be unburned fuel. Meaning that some calories are not absorbed failing the calories in and out equation.
Yes absolutely. Not only that but plenty of our food passes through undigested whatsoever. In theory we can't control that so we can only measure calories ingested, not calories absorbed but it hopefully sheds light on the fact that this is more complicated than just a number