Dark brown discharge on birth control pill

Patient : My girlfriend is 15 years old and she started the birth control pill Microgestin Fe 1/20 about a month ago. This is the first time shes ever been on a pill and she hasn't missed a pill yet, all within an hour each night. She started it on the first day of her last period. We had sex 3 times over the past month and used a condom correctly each time. The first time was a few days after she finished her period. I did not finish inside her. The next day she noticed a light dark brown discharge, and this lasted for 2 days. The next week we had sex for the second time, and I finished inside her. We used the condom correctly and she has been very precise with the pill. After that, she experienced this dark brown discharge again for an entire week, but this time heavier. The day it stopped, we did it for the third time. Note, she started taking the pink "sugar pills" or "period pills" on the Wednesday during her week stretch of the discharge, and we had sex for the third time on the Sunday after that, which was last Sunday. After the third time, she had very light discharge once and that was it. As I said she hasn't missed a pill and we used the condom correctly every time. Is there something wrong? Could she have missed a period, or could the brown discharge have been her period? Is there any chance of pregnancy? Thanks for your help.
Symptoms:  Dark brown discharge
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