I am currently on birth control, i had my period about two weeks ago.. but i am now having muddy like brown discharge. what could be causing this?

Could be:: Breakthrough bleeding caused by the hormones in the pills; could be: vaginal infection or std (yeast, bacterial vaginosis or chlamydia/gonorrhea/trichomonas), could be: ovarian cysts, or polyps in uterus, or fibroids (more common in older women). Could be an effect of stress on your body, or a thyroid problem. If it doesn't resolve, you should see a gynecologist to evaluate.