Typically, when a product is as limited as the limited and ghost editions for Destiny were, the publisher (Activision) provides each retailer with a very specific allocation. The allocations for Destiny were seemingly not provided to the retailers, and the retailers were simply told to begin pre-orders and that they were limited so do it quickly. After the pre-orders were taken the publisher came back and said they were not going to be providing as many as were pre-ordered.
My guess as to why this happened is that the publisher may have been trying a new approach, and just letting all the retailers have a free for all and letting the demand dictate who got what. Not a bad idea, but it obviously failed in practice (failed the customers, that is).
Now another theory (and given the retailers who have been cancelling pre-orders, this is very likely), the retailers continued taking pre-orders after being told to stop by the publisher. In this case the blame falls [i]almost[/i] entirely on the retailer, though the publisher is still not blameless as they did not provide proper allocations.
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It's the second one according to an interview. And the reason they didn't make tons of special editions is because they actually WANTED a truelly limited limited edition. Which I think is nice.