For the moment we're without official confirmation, so we've got our fingers crossed that this is just a clerical error.
We've reached out to Sony and will let you know what we hear.
Update: You still can't pre-order The Last Guardian at Gamestop, but SCEA's Senior Director of Corporate Communications, Patrick Seybold, says reports of the game's cancellation are "not true." So, why has it disappeared from a major retailer?
Update 2: This just in from GameStop: "The Last Guardian has not been cancelled by Sony as we incorrectly stated in an automated call to reservation customers. Because the game did not have a specific release date, GameStop made the decision to remove the game from our system. The Last Guardian will be reinstated for pre-order when a firm launch date is known."