Hi,
Welcome to ehealthforum.
The brown bleeding that you are having could be the old blood coming out. You should get an examination done by your doctor/gynecologist to make sure you are not pregnant while being on the pill (since you missed taking them).
Request your gynecologist to change the prescription for the pill that has lesser side effects and gives you protection from pregnancy. Discuss about alternate methods of birth control like implants and depo shots (to avoid problem of missing the dose). See if you can be put on them. If you miss pill or take it late, follow up with additional birth control measures (condoms/spermicide) if having intercourse.
Take care.