What bad position are they in? No majoras mask 3ds's have become available from another retailer since Best Buy was selling them. So it's not like anyone passed the opportunity to get one because they thought they were taken care of. They are literally in exactly the same position they would be in if best buy had only let them order one. Most likely best buy sold more than they had and rather than cancel orders where only one was ordered, they went after multiples. Makes sense, right? You upset less people that way. Cancel the order of the guy who ordered ten instead of nine people who ordered one.
It's easy to say that, but you don't know any of the circumstances. For example, what if i had 2 children and I ordered 2 and paid for both. Then, I told my children "Look at this amazing new 3DS XL I ordered for your Birthday. It's a special edition from your favorite video game series Zelda!". I could use a similar scenario for my Wife and Myself. Look sweetie, I just ordered us both a new 3DS XL. Look it's from Zelda, our favorite series!
Now that Best Buy cancels it they could be in a position to have to explain that they both aren't getting the new 3DS XL that they were told they were getting.
The point is, you, I, or anyone else doesn't know the circumstances in which some of these orders were placed and this could hurt legitimate customers who's only intention was buying it for themselves or family.
As I mentioned above, I understand what they are trying to do, but it would have been better to limit the orders to 1 per address/account/IP/whatever from the very beginning. Honestly, it's really unfortunate how these pre-orders have been handled and taken advantage of. I truly hope Nintendo starts offering these types of items similar to the n3DS Amassador Editions in Europe.
Edit:
Full Discolsure, as I mentioned in my first post in this thread, this doesn't affect me as I did get a Pre-Order in at Gamestop.