Scientific American writing about how the types of food, the method of cooking (or lack thereof), the microbes in out bodies, the immune system, and the type and processing of certain foods might affect the amount of calories in a given food:

For one, our bodies seem to expend different quantities of energy to deal with different kinds of food (the energy expended produces heat and so is referred to by scientists as "diet-induced thermogensis"); some foods require us to do more work than others. Proteins can require ten to twenty times as much heat-energy to digest as fats, but the loss of calories as heat energy is not accounted for at all on packaging.

For another, foods differ in how and where they are digested in our guts. Some foods such as honey are so readily used that our digestive system is really not even put to good use. They are absorbed in our small intestines; game mostly over. More complex foods, on the other hand, such as cassava or almonds, have to travel to the colon where they meet up with the largest concentrations of our little friends, the microbes. Digestion continues with the help of our trillions of microbes but nutrients are shared between us and them. The microbes help to break down many compounds our own bodies cannot and in doing so go on to produce a mix of more microbes, gases (such as methane) and then fatty acids. The accounting associated with this process of sharing with the microbes is not considered in calorie counting.

In most cases, raw foods were lower in calories when cooked.

Food for thought.