other than taking them off and remeasuring and resewing them on, you could take the seam out from the center toward the corners till you come to areas that are not wavy, then take a seam in the center to make it fit. then resew back on.
usually you measure the quilt top in the middle-that will be the measurement of the top and bottom borders. then later measure the length down the center, that will be the measurements of the side borders. just add seam allowances. place the borders on, matching centers and corners and pin. then sew.