that's a type of defect commonly found on LCD screen, a bit similar to dead pixel

you should have request for the exchange/repair on the spot when u bring it back to the seller as it's still considered under their 'limited' warranty

but since it's already past the 6 months of their limited warranty period, nothing much you can do about it beside sending it over a reputable shop to replace the top screen, or to save the hassle, just get a new one

and don't forget to post up the name of the vendor/seller you got the 3DS from, blacklist them