The thing that comes to mind for me is that they have, or had an employee that was not on the up and up and was planning on taking these, plating them offsite and selling as gold.
APMEX would never divulge something like that, but these kinds of errors are not common, they are out of the realm of possibilities without some prior planning.
(as another poster said, the size of the gold and silver bars are so different, in relationship to the dies that would be used)
it would not be possible without a deliberate attempt.
My guess is someone got caught, but not before a few made it out of the factory. Possibly the mint that has the contract to mint those bars for APMEX. Something broke along the way, and it leads back to the manufacturer.
APMEX will now be running damage control, especially since the original recipient of the said bars decided to go public with the error.