Yes, there's no doubt in my mind it happened at the Mint or where ever the Mint does their packaging putting these proof sets and other Mint produces together.
I could say that there is terrible quality control and all the mints. But, the Mint has done hundreds and hundreds of millions (probably trillions) of these sets and other Mint produces over the years. Problems, mistakes and errors are bound to happen.
But when you see things like these, you have to ask yourself.......is the Mint production area like a construction site?? Yes, it's a small rock or stone!!