Another example I give is have two people eat an exact 5000 calories a day and the same amount of physical activity. But one person also eats a full measure of ExLax with each meal and the control does not. If you measured all the calories in and all the calories out they would be equal. Of course you would have to measure the calories pooped out because the one getting the three times daily ExLax would be pooping out most of his energy rather rapidly. The poor guy on the ExLax diet would satisfy the law of thermodynamics where energy in has to equal energy out just like the guy on the regular diet. But one of them might be putting on body fat while the other is losing weight because of poor nutritional absorption. So while it is true that energy in has to equal energy out it tells nothing about what the body does or does not do with the energy.

Another example would be to have a scientific test where two groups of people all eat isocaloric diets where one group eats normal food but the other group eats only sawdust. If it was 5000 calories the sawdust in a Bomb Calorimeter would measure 5000 calories. So calories in has to equal calories out (assuming the poor subjects on the sawdust diet lived). In this case the people on the normal food might gain weight but the sawdust group should also gain an equal amount of weight if the calories in/calories out mantra is true. The point is, a calorie is not necessarily a calorie in relation to what the body does with it. A calorie of meat does not metabolize the same as a calorie of sugar. A calorie of fat does not metabolize the same as a calorie of fructose or alcohol. 

The food industry likes the "calorie is a calorie" mantra because it lets them sell bad food without a stigma attached. When a person is only worrying about "calories" a calorie of Coke is the same as a calorie of broccoli. But it is completely different. In the Coke the fructose gets ported to the liver to be processed there (and like alcohol cause a fatty liver if too much consumed) whereas a calorie of broccoli has to be broken down in the digestive track using lots of energy up doing so.

A calorie is a calorie when burned in a Bomb  Calorimeter. Calories are not equivalent when it comes to producing fat on peoples bodies. Some are metabolized completely differently than others. What and how often we eat makes a lot more difference than just the amount of calories we eat.