Nope, shouldn't hurt the bones around the girly bits. Have you tried playing with the angle and/or position of the saddle? If not, give that a whirl. Try angling the nose down a little and maybe move the saddle up a tiny bit in the rails (maybe you're sitting too far forward in the saddle?).

I had the type of pain you're describing with a saddle that had a cutout. There was just too much pressure on the area around the girly bits. Nothing helped, I eventually got rid of it and found one without a cutout that I liked. But, I would suggest playing with the a little before moving on to the next since everything else feels comfy on it.