Are you talking about the every so slight bumpiness? That's quite ok. It's not harmful to the tortoise at all, and just adds to her beauty. There's no sense in going over all the 'woulda', coulda' shoulda' at this time. Try to provide your tortoise with a bit more humidity in its life and the bumpiness shouldn't get any worse than it is. It's a beautiful shell.
Or are you talking about the vertical creases that seem to go from the center of a scute down to the seam? That's normal too. Nothing wrong with that at all.