1) hope you're not doing them with straight legs - strains the back
2) hope you're not keeping your head straight - strains the neck
also, you don't really need to go beyond a crunch - after that one tends to use the legs
also, doing them smoothly, right? no jerking. slowly is better work anyway
you might have put your back out - lumbar or cervical vertebrae. Would need to see a chiropractor to sort it out. You'll know if you've put it out because certain turning of your body, or attempts to lift something, will cause shooting pains (extreme) in your back.
best homemade exercise to help the back is to lie on your back flat, raise your legs to the ceiling then grab your toes. Forms a kind of arch with your back, on which you rock gently to and fro. Basically run the length of your spine along the floor, preferably a carpet / not too hard. The shape of your body is like a U - except fingers grabbing the toes. keep the legs as straight as possible.
IMHO