Brown spotting for 3 days, missed period, took two pregnancy test a week apart say neg and when i pee it hurts my right side really bad? what's going on ?

Pain on voids=UTI...: Until proven otherwise. Need urinalysis. Sometimes an std gives a combination of symptoms like these. Needs a closer eval by a physician to avoid worse development like kidney/blood infection or pelvic inflammatory disease.

Agree with Dr. N: Your symptoms are consistent with urinary infection. You need to see a doctor for treatment.