if it's 2 layers (1/4") it shouldn't shrink. if it's less, then it will. not much you can do about it. going slowly may help the matters, but probably won't eliminate it.
Are you grinding the edges before you fuse? If not, you may have areas where there's only 1 layer of glass and that will shrink up to its equilibrium thickness.
Are you firing too high? This will leave sharpies on the edges.