Unfortunately, this is how it is. There is no central warehouse you are ordering from - you are buying from a specific store location. And that bass might have been in someone's hands bring tried out when you bought it.
Not sure when the store gets notified that the bass has been bought online and should be pulled from the floor, but obviously its a very flawed system. And again, one store might be good at doing that while another sucks. Or one employee at one store is good at that and the days he is off, the other guys don't even bother to look.
It paints a picture of a larger issue - but again, GC is treating their inventory as a whole bucket while it is spread out over all their stores. And their main business isn't selling used gear - so its an afterthought.
At some point they realized that with all their used instruments at all their locations, it would be easier to sell if they marketed each piece of used gear not just to that store's region, but to the whole USA. Someone had the bright idea of databasing their used inventory and taking pictures and a brief description. They even implemented the ability to purchase the item through their webpage. Unfortunately while that's where the logistics are only starting for online shops like Amazon, GC seems to have stopped there. Once they take payment, its a crapshoot if you'll actually receive the item, if it was even still available (and not sold 2 weeks prior and webpage manually never adjusted), and then what actual condition the item is in.
I highly doubt a store's POS system is tied in to the entire's company's inventory database - so there's a manual step involved, or many, to go from an online purchase to actually receiving the item.
Compare that to their new item sales through their webpage. They have a warehouse full of gear, and when you order online, it should update the warehouse quantity and initiate the process of pulling the item for shipment.
Places like Amazon make it look easy, from a consumer's perspective - but they have a LOT of systems in place to make things run that smoothly. GC does not. Their used gear selection seems like a good idea with no budget to make it work effectively.
Best bet is to call the store before buying it and try to buy it over the phone. At least then you'll be talking with the person who has the item and the item is in their database. Skip the online queue.