A friend of mine did that --- didn't discover it until he'd had the quilt almost totally quilted. It's not easy to take a quilt off the Longarm and get it back on with the same tension!!!!
I learned from his lesson.....I always lay the backing on the floor, then the batting and then the top....JUST to make sure my measuring isn't screwed up! Also...I put a tiny mark or pin at the top center of each piece. That way I don't turn one of them sideways....and run out of fabric or batting.