Hello, Thanks for sharing your health concern with us. The emergency contraceptive pill contains high doses of progesterone and this leads to hormone disturbances. This is the most likely cause for the brownish discharge observed. However, pain is not an usual accompaniment. She was in her fertile phase during the intercourse. It is likely that ovulation may have occurred. Though, she is well protected since she took the pill soon enough. Please wait for her next natural period and if she becomes overdue by ten days, get further help. If you wish to test earlier, you can opt for the blood test for pregnancy. Hope this helps.