If you've lost weight but noticed an increase in body fat, you could be in the later stages of exercise overload. The body responds to prolonged stress by elevating levels of stress hormones, including cortisol, Stenstrup says. Over time this will lead to increased storage of adipose tissue, as well as inhibit steroid-like hormones that normally help increase muscle. A decrease in muscle mass can cause you to shed a few pounds, but this isn't a good thing since it means your body's less efficient at burning fat.