When you eat fewer calories than you burn, your body will go into starvation mode and quickly store any excess calories around into fat, producing stinky Ketone bodies in the process.
While your net calorie intake may below what you burn, you probably eat in large meals, right?
After the large meal, your body is flooded with calories. Since you're in starvation mode, your body will convert all the immediate excess calories into fat. Then, several hours later, you run out of food to burn. The thinks its starving again, and in order to preserve life, turns down your metabolism. As a result, less calories get burned than fat you put on during the meal.
How do you prevent this vicious cycle? Maintain an active lifestyle so your body has no chance to turn down your metabolism, and the fat will come off much faster.