If I get a wave in a border after sandwiching, I have picked out a seam and carefully invisible ladder stitched a new seam removing the extra fabric. If it is wavy before sandwiching, I remove the border and fix it. I rarely have wavy borders as I measure and pin the top to the required measurement before sewing.
if I was machine quilting a charity quilt that had really bad wavy borders, I would quilt a piano key design and put the “ dart” under the line of quilting.