Id put some more stain on it and let it set for 15-20 minutes to see if that helps. If not, do as Mojo said and put stain on it and dont wipe it off so thoroughly. This could be caused from either wood characteristics or it was sanded a little bit better there than the rest of the peice sealing the pores and not letting it stain as dark. When Im prepping for stain I try not to sand too heavily to bring the wood to a fine smooth finish. I leave it a tiny bit rough to insure even staining, then apply two coats of varnish to seal it, sand it smooth and then finish varnishing with another couple light coats. Ive had my best luck with custom work following this method. Every time I went nuts presanding and then wiping with a tack cloth, I ended up sanding it down after a couple coats anyway. I dont even waste my time with tack cloths anymore. I blow it off with the compressor and I'm on my way to varnishing. Good luck.