Perhaps you can buy a free book or free app and then check to see if it does two transactions.
What happens normally is that there will be a first charge to check if you have money and then a second charge. Perhaps it got confused and charged twice.
That happended to me too this weekend. I bought a book and my gift card was double billed.
I called customer service and they refunded one.
I have bought over 200 books from B & N and this has happened maybe once before.
I have purchased an e-book subsequently and was only charged once, so I do not think you have anything to worry about. But you should always check no matter where or what you buy that the charges go through correctly...