Sometimes figure switches are done by customers who then return the older, less desirable character for a refund. It might have been perpetrated by a store employee and that's happened for sure, but as a SW collector I've seen and heard a ton of truly disappointing and irritating stories of collectors who find the figures they've been hunting for only to find out that somebody bought a Darth Malgus or a 6" Greedo, removed them from the packaging, put an old Darth Vader from the beefy "Steroid" era or a superhero character in their place and then took them back to the store to get a full customer refund.
And since most customer service and returns employees don't know Darth Malgus from Death Metal they just make sure an object is in the packaging, refund the customer and have it sent back to the toy department for reshelving. It blows but only some very alert and knowledgeable employees can stop most of this.