Hiya, from what i understand the brown/reddy discharge can be caused from the contraceptive pill but this is supposed to settle after the first few months, if it doesnt it could be that the one your taking is not working well with your body and you may need to try another one. The pain however may be endo, i had my pain in my lower abdomin and sometimes you can get other symptoms like irregular periods and feeling tired all the time? Hope this helps.
I have has similar problems with breakthrough bleeding when taking bc back to back. I have had brown nasty bleeding for up to 28 days straight. They said its normal to have breakthrough bleeding for three months. I dont know If this help. If your uncomfortable with this just keep in contact with your physician or get a second opinion.