What you're describing is not what happens on a normal purchase and, had I been sold a load of garbage like you were by whoever you were on the horn with, it would be immediate rockets to his supervisor. I hope that what he told you was pure BS. Your solution is to talk to B&N again and, if needed, escalate it.
Try to get another bite at the apple, another try at a download. Just to be on the safe side, run a 'hard reset' first (press/hold both Home and Sleep/Wake for 10 secs until Apple logo, then release and let boot complete) before trying the next purchase and download. If it still happens after that you'll have to start out by suspecting either your install of the Nook app or, perhaps, that file itself.
So, as a test, I just bought a book on Nook (just a 99¢ special but one that I'll like reading, I think) and it worked as expected. Open the app, tap Shop, find the book, order, confirm the CC info, and it was done. A minute or so later it popped up on the Nook library display, marked as 'Lendable', and right after that it was being read. The introduction, at least.