That's not necessarily a bad sign. Crunches are kind of notoriously bad for your back. Some people actually say you should never do them, though I'm not gonna go that far. I'd guess you just have weak back muscles and iffy technique.
The best way I've ever found to work out my core is just by doing full body work that uses it. But if you want to spot train, I'd suggest doing things other than crunches to strengthen your abs and back. Some ideas you could google: supermans, v-sits, tuck-ups, bicycle kicks.
Also, might sound weird, but something that helped my core strength and stability a LOT were headstands/handstands. Start with tripod headstands, go to yoga headstands, forearm stands, etc. Just make sure you have technique right at each step and can hold for a while before you move on.