Hi,
Welcome to ehealthforum.
The brown discharge and cramps after 2 weeks of periods could be due to possible implantation bleeding if you have been sexually active after your periods. It can also suggest possibility of infection if it is associated with foul smelling discharge, itching, burning or rashes.
Visit your gynecologist/obstetrician for further evaluation and tests to confirm the exact cause. If infection is detected, get your partner also treated simultaneously to prevent chances of re-infection, and avoid intercourse while being on treatment.
Take care.