Had period 3 days late with light brown discharge. What could be wrong?

Uncertain. Brown discharge is likely older blood being cleaned from the uterus. Reasons for missed / late period include: an anovulatory cycle in which no egg is released, marked v or ^ in weight; eating disorder; over-exercising (endurance athletics), travel, significant illnesses, oral contraceptives ; other meds, illegal drug use, breast feeding, hormone imbalances and medical problems (i.e., pcos).