I just finished doing some staining on some maple. It turned out fine. The only time this has ever happened to me was when I tried to short cut the prep work before staining. One reason it turns out like this is because you have to make sure you have done enough sanding. The rough areas will really hold onto to the stain, more so than the smooth areas. I am not an expert on this subject, I have learned this from personal experience. Just a suggestion.

As you mentioned maple is difficult to stain. You really need to use a sealer before staining if you prefer an even look to the finish. For the parts that are already stained it's too late to do anything short of sanding them down and starting over. That would be a tremendous amount of work as the stain in the darker parts has penetrated more deeply and would require a lot of sanding to lighten back to the original color. If it bothers you deeply then it would probably be easier just to remove and toss the pieces you don't like and start fresh.

It's hard to tell from your small photos, but the dark areas actually appear to be from figure in the maple rather than blotching. I actually like contrasting figure in maple and think it has a lot of character, but that's just MHO.