People self-report they did "all the right things" and when checked found out they undercounted, cheated, etc all the time.
In fact, the article says "He kept to low-fat, low-calorie food for three years. It simply didn’t work. At one point he lost about 10kg but his weight rebounded, though he still restricted his calories."
Keeping a diet like low-carb or low-fat etc (and other fads), is difficult, so many rebounce.
But the true lifestyle change of a balanced diet is difficult anyway too, and most can't do that either.
(And you do need a balanced diet, whether you follow the calories/in out or not).
This doesn't invalidate the calories in/out, just their ability to apply it (and it's not necessarily their fault, they can have all kinds of impediments causing them to overeat, eg. situational depression).
On the other hand, if you know 100% your calories, you can diet even with the most surprising foods:
http://edition.cnn.com/2010/HEALTH/11/08/twinkie.diet.profes...