Hi!
She is probably having break through bleeding as a side effect of the pills. BUT I ALWAYS recommend a pregnancy test. If the pregnancy test is negative, and if she has been taking her pills faithfully, I expect that you are in the clear.
I think the two of you sound very responsible! Make sure that you have an extra condom on you at all times--you just never know!
Good luck!
Dr B
PS also, don't forget about Plan B also. I think that would be overkill for this situation, but it might save you some worry down the road.
Brownish spotting can be normal. Sometimes it means she is about to be on her period or is still coming off of it. And normally if you were to impregnate her she wouldnt be experiencing anything like that on the third day.
-Toni.