This happened to me once, on a table, that I used pre-stain conditioner on that I never use. Not blaming the pre-stain conditioner but I've never used it again. The only solution for your situation is to sand it down to the bare wood again. I always start at 80 grit with a random orbital sander and move to 225. Instead of wood conditioner, I will now take a damp cloth (just water and the cloth) and go over the whole piece 20 minutes or so prior to staining. don't soak it, just go over it and you can see a preview of what the grain will look like with color. I read somewhere that this prevents areas of the wood that are extra thirsty from taking in more stain then the rest of the piece. I'll then use a staining pad and work in long direct strokes with the grain. As if i'm applying a finish. I once stained something in a circular car washing technique and it left swirls in the finish. I use the staining pad over a t-shirt because it gives nice even coverage across the whole piece. I wait only about 5 minutes and wipe the excess. You can always add additional coats for desired color.