Hi there. I've had three pregnancies and six shots for being Rh Negative (oh yay). The spotting isn't necessarily from having sex or not having the shot. I bled heavily one day with my first pregnancy for no good reason. And for my third. It's just something that happens sometimes and the doctors didn't have any good reason for it.
And while you might have known you're Rh negative, your doctor did. Your doctor knows your blood type. It's in your records. So s/he'd know if and when you needed the shot. It wasn't up to you to know you were "Rh negative". All that means is you have a negative blood type so your body doesn't have the Rh that positive blood types have. That's what makes blood either positive or negative, the presence or absense of Rh. There's a concern that without the Rh shot, your body would develop antibodies that would attack any future positive blood type babies you might become pregnant with in the future.
You'll also get a shot after the baby's born, either right after delivery or at your six week checkup. I can't remember which it was for me. And every time you get pregnant, you'll have to get the shot to prevent your body from developing antibodies. And also after the baby's born if the baby is a positive blood type. HTH