I have Bmr's lowering springs and Bilstein HD's on my car, and when I rotated my tires yesterday, I noticed a spot on both sides of the rear end where the bumpstops had rubbed the rust off. Is it normal for the suspension to hit the stops on a lowered car?

 

Yup. That's what they're there for. Road racers and autocrossers are on them all the time. To stay off them, the car would be unimaginably stiffly sprung, or jacked up too high.