To illustrate with an extreme example, lactose is a sugar and carries energy, but some people can digest it (and their bodies will get the full complement of calories from it), and some people can't (it'll get digested by bacteria and they'll get gas and feel unpleasant; I'm pretty sure they don't get calories from it). It is incorrect and stupid to say that an item of food with significant lactose component carries "N calories" without specifying whether the person who eats it can digest lactose. Likewise, with cellulose, I think cows get a lot more energy out of cellulose than humans can.
Also, it seems likely to me that people's digestive systems' performance varies with "outside" conditions in the body. For example, I've heard that being pumped full of adrenaline puts digestion on hold; and subjective experience suggests to me that if you eat a lot of food (over a period of, say, a day), your system will send it through pretty quickly, without digesting it fully.
I suspect there are a lot of other situations in which one's body doesn't get all N calories from an "N-calorie" item of food. I suppose that if that happens, then the remaining part probably will be digested by bacteria, and one may notice symptoms of... oh, hey, there's a name for this, "indigestion". (Though if the amount of left-over energy is really small, then the symptoms are probably too slight to notice. If 10 or 20 calories a day matters, then this may make things unpredictable.)
I suppose one could count the bacteria digesting the food that you didn't as "calories burned", but then that means you may be burning a bunch of calories without doing any physical activity.
Does someone more knowledgeable than me know a) whether these things are really significant and b) whether these researchers take them into account?