Thank you for your query at DoctorSpring.com.
The brown discharge is most likely your period starting early. This can sometimes happen with the hormonal contraceptive pills as a side effect and stress etc can also have an effect on this.
There is practically NO possibility that you could be pregnant. I say this because of the following points.
1. You have already had your period after the last intercourse. (This 1 point alone is sufficient to rule out pregnancy)
2. You are on contraceptives plus the intercourse was protected. This make conception impossible.
3. Pregnancy tests are negative.
So please relax. You have no reason to worry.
Let me know if you have further queries.