MFP calculates your calorie needs based off your height, weight, age and what you set your activity level to. then they deduct about 500 calories a day from your total, to give you a deficit everyday. When you exercise, you expend more calories so mfp adds those back in so you eat them.

Im not sure what your stats are, but lets say MFP set your target calorie goal at 1200 daily. then you exercise and expend 400 calories. If you only eat the 1200 mfp set, minus your 400 exercise calories, then you've only netted 800 calories for the day. 800 calories is almost always too low to give you the energy and nutrition you need to keep up your new lifestyle change.

there are obviously many things that can change the above senario, including PCOS but that's a brief overview of how mfp works.