Brown discharge two days after period ended...

My cycle ended on Saturday. I had protected sex on Sunday night. The condom broke before ejaculation. Although, we are both way outta practice, it lasted well over an hour... The next day and still going (three days later), I started to notice my cervical mucus is tinged slightly brown only when I wipe. There is a little discomfort. Does anyone have any ideas? Did we possibly damage something? Or could this be residual blood from my very recent cycle? Thanks in advance...