The method most commonly used to assess the number of calories in foods is flawed, overestimating the energy provided to the body by proteins, nuts and foods high in fiber by as much as 25 percent, some nutrition experts say.
“The amount of calories a person gets from protein and fiber are overstated,” said Geoffrey Livesey, the head of Independent Nutrition Logic, a nutrition consulting company in Britain, and a nutrition consultant to the United Nations. “This is especially misleading for those on a high-protein, high-fiber diet, or for diabetics” who must limit their intake of carbohydrates.
An adult aiming to take in 2,000 calories a day on a low-carbohydrate, high-protein diet may actually be consuming several hundred calories less, he and other experts said. Calorie estimates for junk foods, particularly processed carbohydrates, are more accurate.
Source: On Food Labels, Calorie Miscounts
Part of the problem is that calories are traditionally measured by burning food and measuring how much energy it takes to get the food to boil water (basically, it operates under the assumption humans are steam engines).
There’s been scientific papers for years pointing out that calorie counts are not accurate, and that even relying on them for any measure of health even when they are accurate may be completely irrelevant to human health.