I put a sealer on not a stain, if that makes a difference. It was water based. I also put two coats on. Not all the boards are peeling maybe I didn't put the sealer on to thick on these boards. It is the boards that are peeling not the sealer.You might have put the stain on too thick. You will probably need to remove it all, let it dry throughly and try again.
Did you wipe off the excess and any places it puddled? A few light coats are better then one heavy coat.
Did you put anything on top of the stain?