Hello, Im 20 Years Old And I Was Diagnosed With

Hello,
Im 20 years old and i was diagnosed with Endometriosis last year. I forgot a pill in August 2 but I took 2 instead the next day. Brown discharge was spotted but it was in small amounts. About August 18 larger amounts of brown discharge started to show and a few days after red blood appeared but not in the same amount as a normal period. Few days after, i decided to take 2 pills a day for 3 days, but that didnt maintain the brown discharge. Today it is September 15 and brown discharge is still occuring!
How can i stop this discharge from happening?
PS: my gynocologist told me that i should stay on birthcontrol pills without stopping them to get periods in between each pack.