The way the muscles are attatched, some of the lower back muscles actually can do that motion, before you start the crunch be sure your pelvis is rolled back....
when you lie flat on your back, knees bent an feet flat on the floor, your pelvis can still be "tipped forward" pretend it is a bucket of water, pull it up toward you, rocking it back, to keep this problem from happening. if this doesn't help it is obviously something else, may want to get it checked out.
I would also advise to do some pilates etc. to strenthen the core all around first, especially if you still cannot do the crunches. Do stabilazation (super mans, planks etc.)
But you are right, nothing shoudl actually hurt, so dont' do it if it does...