Around 2000-2002, you could walk into most B&N stores and find nice comfortable chairs to sit in. These chairs encouraged book lovers to grab a book, sit down, read a few pages, and actually enjoy the book buying experience. So what did B&N do over the next couple of years? Get rid of the comfortable chairs, and replace them on a 1:2 basis with hard, uncomfortable wooden chairs. Then slowly phase these chairs out completely.
This did a couple of things; discourage people from reading books on the book floor, while encouraging them to read in the Cafe, where the books and magazines get damaged easily. But the core idea of having an inviting bookstore died that year.
Another issue was the Cafe relationship with Starbucks. The Cafe's use Starbucks components, and often follow their recipes. They have tons of "Starbucks" branding as part of this relationship. BUT you can't use a Starbuck giftcard at a B&N Cafe. Try explaining this to someone who received a giftcard over the holidays. They order a coffee after waiting in line, and get hassled about the form of payment. It wouldn't have been hard for B&N management to work out a deal with Starbucks for handling these cards, but B&N never did.
Also, bookstores have the ability to send a majority of their inventory back to the publisher (yeah, crazy legacy stuff). Inventory levels are largely decided by Corp HQ yet despite modern inventory mgmt software being a thing, they continually botched it. So you would get huge shipments. Then when cash flow for the company would get tight, they'd have you pull the books off the shelves and send them back to the publishers. This would be a continual process that consumes tons of time, time that would be better spent on customer service.
Corp HQ would also decide to change the store layout frequently. The staff would pack up all the Sci-Fi/Fantasy books, move them to a completely different part of the store. Customers would come in, head to their favorite section, and be flummoxed. Since so many labor hours were spent doing this type of thing, (and the aforementioned book pulls), there weren't as many employees on the book floor to help. I called it the Titanic chair shuffling...
Staffing levels were always a problem. On busy holiday weeknights, you might have 4-5 people working. One manager, one head cashier, two in the cafe, and one on the book floor. Employees need breaks, so often you would end up with one cashier, and one person on the book floor. If you get a rush of people, that line at the register can get awfully long. B&N only pays lip service to the customer experience.
A lot of these types of decisions add up overtime to create a crappy customer experience. B&N never could compete with Amazon on pricing, and never should have. They should have embraced the book buying experience, and made customers love coming in. But that's a long long game to play, and their management made continually bad choices (like Nook) that distracted them, took capital they didn't have, and confused customers.