I had the same problem. I got 2 emerald crabs as well. The emeralds left it alone if it was bigger than a BB. If it was smaller than that, they chowed down on it. So I just waited until all the BB sized bubbles got a little bigger and plucked them out of the tank. A few of them popped, but that was no big deal. That just gave the crabs more to do.
Don't let them get too big before you pluck them out though... The bubbles can really wedge themselves into the rock work as they get bigger.