I would unstitch the seam between the dark blue and the other floral, smooth out the extra fabric (trim if necessary)and use an invisible ladder stitch to make a new seam. Is this the only spot? If not I suggest instead of a continuous line of quilting where the extra fabric advances until it forms a bump, try quilting stand alone motifs (flowers) along the borders. This allows for a little extra puff between motifs that can disguise any problems.