Hi Kevin
Dip a corner of that scrub pad into a solution of 1-part ammonia to 10-parts water. Hold the saturated corner over the bad spots for a few seconds, and then lightly scrub. The Stain is still pretty fresh, so this should do it. You should also be able to preserve the Stain in the joint, since it has a better bite on the grout, than it does on the tile. Worst case, you will have to touch-up a bit. I imagine you have the technique down pat now, so a minor touch-up will be a breeze.
This only applies since the Stain & Seal is fresh. Once it cures for a week, or so, Methylene Chloride and MEK are they only chemicals that will completely remove it.