The wood has been sealed by the clear finish. This finish penetrates into the wood sealing the stain in the process. The best way to deal with is to find a <a href="//www.painters-toys.com/wood-stains/stain-touch-up-pens.html" target="_blank">stain touch-up pen</a> or use a thicker stain, same color, and a artist brush.
Work just the scratch and blend by dabbing with a clean soft cloth around the scratch.
You could also try applying your stain with a q-tip, dab to blend then add more when dry.