What you're seeing is sap/resin from the wood. Sorry, I think you're out of luck in getting a refund. Knots tend to bleed. The usualy remedy is to simply replace the board. Then, let it/them cure, and re-stain. In a couple or so years, the stain will wear off, and when you stain it again, they should all look uniform, so to speak.
Don't sweat it. I think the rep is right, especially if you're only seeing it with the planks that have knots. Stain/sealer won't prevent the wood from bleeding the sap/resin.