That's not a factory mistake. That's a cheap skate who returned the package with the wrong figures in it.
I'd say that it's more likely an error from the factory. Both sets were in production at the same time and it's not unknown for something to slip out in the wrong packaging. If it had been, say, Aquaman and Black Manta in the box it would be far more likely to have been a figure-swap.
That said, I still wouldn't recommend it for an attempted re-sell. Very limited collectors market for mis-packages and would be a much easier sell if it had been Joker and Harley in the wrong box than Cap and Adam.