Can you describe these spots? Are they large and/or small? ARe they random or in the same 'area' in relation to each other?
My first guess is that the stain wasn't properly mixed. In short, it's suppose to be stirred, not shaken. And, it's to be stirred OFTEN. If as little as 20 minutes goes by, it can start to 'settle out' and you'll get an uneven coating because you're picking up 'solids' from the can/pan as you do your staining. The only way to get rid of it is to re-sand (which I'm sure you don't want to do.) Perhaps, if the spots are 'in the right places', you can cover them with furniture or runner rugs or area rugs.
Sorry, I can't see the 'problem' from here but that's all I can think of. My best to ya and hope this helps.