Maple, even when prepped to perfection, does not take pigment stain well and can appear blotchy. You could try re-sanding, making sure to get all the old finish off. I'd also recommend sanding no higher than 220 grit preferably with a random orbit sander. Pigment stains need the little nooks and crannies to settle in, otherwise the stain will not have any effect, and the RO sander helps get a nice even surface for staining.
Alternately you could re-sand, seal and then use a spray on toner (Guitar Re-Ranch has a nice product so does Behlen - which is often available at Woodcraft retail shops.)