They absolutely could have done something - they either failed to make the right customer service decision and sell the merchandise to the guy on site, or the company failed to set up adequate systems to prevent this scenario from occurring.
I worked for a retailer with 'buy online/pickup in store,' and if we got an order over the computer and the merchandise was in a customer's hands on the sales floor, they would at least get right of first refusal. We only accepted CC or paypal for online orders, which both allow automated refunds for online orders that couldn't be filled, and to me its worse customer service to alienate someone physically in your shop, rather than someone buying online. Not only that but you miss out on the opportunity to throw in some strings, cords, picks, whatever else. You can't overestimate the importance of face time with the client, not to mention the potential negative impact on social media like this thread.
The way it would go for us was the customer ordered the item, we got a notice on the computer, then we picked and processed the order, removing it from the sales floor, and THEN the customer got a confirmation email that it was ready for pickup.
The systems retailers use should (and usually do) allow for the inherent lag between me sitting on my computer clicking some buttons and people running a sales floor where they have other responsibilities besides constantly checking the computer, picking the merchandise, and processing online orders. I just checked out a pedal that is in stock at my local GC and if I order online I won't be able to get it for 3-7 days, so it seems like they allow some kind of processing time.
At my store, if 6 hours went by from when the order was placed and we did not do the step to pick it (i.e. hold the merchandise off the floor,) the customer's order was cancelled, and all money refunded. This happened pretty often, with the usual cause being another customer bought it before we could pick it.
It's possible that GC has similar systems and this store just blew it. In that case it's 'this guitar center at it again.'