We still have our periods when we're using birth control pills. And like emma said, the pill actually causes spotting.
After using the birth control shot (depo-provera) for a while, some women stop having periods until they stop getting the shots.
It was most likely spotting caused from the pill. But she may have been at the very end of her period too. Menstual blood is not always bright red, sometimes in the last day or two it turns darker, even brownish.
Personally, there have been several times that I thought my period was over (because the bleeding had stopped for half a day or so) and then I would have sex (gentle or not) and start bleeding again.
In my opinion she is completely normal. But it's good that you are practicing safe sex and are concerned about what is/isn't normal.