I have had that happen many times. Usually I have either stretched the backing fabric too much (I usually use fleece) or I didn't stretch it enough. I don't think it's a problem to lay it out, stitch around, and then trim after, but I do think you need to pin the heck out of it and maybe tape down the bottom layer to make sure there's no shifting.
In my worst case, on a lap quilt there was a huge ripple down the back of the backing. I was almost in tears. Finally I took a deep breath and cut the ripple, trimmed off the extra, and sewed a strip of fabric all the way down the quilt, covering the cut. It actually turned out okay, as it added color to the back and looked intentional. But it is not a happy memory : )
Laurie