It isn't as easy as eating fewer calories than you burn or a calorie deficit.
Some foods have a higher glycemic index or glycemic load than other foods. Eating these at the wrong time, when not exercising, can cause the body to store it as fat. We all know that fat is more difficult for the body to use as fuel.
You can run a calorie deficit and will certainly loose weight but you will see vastly better results if you eat high glycemic foods only during exercise and eat low glycemic foods apart from exercise.
For example, one shouldn't expect stellar weight loss results if they are eating white bread and drinking sweet drinks for lunch while working a desk job or having sweet snacks before bed. These will surely be deposited as stubborn fat which the body prefers not to burn.
-Tim-