there should be something to take that out but if not, i think a ribbon that matches as closely as possible the red background...and then go in w/ the same color thread and do a similar tight stipple on top of the ribbon. it would be subtle tonal effect that might even enhance it without detracting from it..tone-on-tone effect. Another option might be to applique 7 slender "pedals" to cover the marks w/ the same yellow square in the center. Add more petals and it could look like a pointsetta!