Bookstores do not mark-up the price of the books. The publisher sets the price and we get a discount, usually around 30- 40%, when we order them wholesale. The reason some places can sell them cheaper is either that they buy them in huge quantities for their own warehouses and pay their workers poorly (B&N) or they make ZERO profit off selling books at all and pay their workers even worse (Amazon.)
Also, if an indie bookstore can't get the book you want around the holidays, there's a good chance that Amazon ordering WAY more than they will ever sell and holding them in warehouses in case the book gets popular is the reason. Then Amazon returns everything they didn't use to the publisher in January, f*****g over the publishers who may have put out the money to print more copies they didn't need, the authors who could thought those books had been sold, the wholesale warehouses who now have no space for new releases, and booksellers who dealt with a*****e customers during the busiest time of the year.