Ow! That was a long wait for a disappointing result, wasn't it? Maybe there was controversy ("That can't be fake - check it again!") or even internal argument at PCGS. I suppose there could be other reasons for that long a delay, but one might be that determining authenticity required more than usual resources. Perhaps other examples needed to be examined? PCGS and the owner know, but I don't.
It did remind me that counterfeits are an ever present danger and that today, it's not just the coins: PCGS holders are also counterfeited. For example, on that link you can see a counterfeit 1893-S Morgan in XF45. It's in a counterfeit PCGS holder, too.
If you look up the cert number at PCGS, you'll find that it is indeed that date and condition. You can also see that it was last auctioned in 2009 for $9,200.00.
If you clicked through the auction link, you can see a picture of the real coin. Even a very quick look should convince you that the fake looks nothing like it, so you could have avoided a costly mistake there.
But there are not always pictures available. Neither PCGS nor NGC takes pictures by default. PCGS offers imaging at $10 per coin and NGC offers it at either $5 or $15 (depending on quality), but few people take advantage of that. If the coin you are looking up hasn't been in a major auction, you may have nothing to compare it to!
That's a shame, because even a crappy photo might well be enough to save the day. I wish all grading/authentication included at least basic photos. It would also be very helpful if they included a photo and precise dimensions of the plastic holder and an accurate weight of the item after encapsulation. Those inexpensive bits of data would make passing counterfeit slabs more difficult.
We can't stop counterfeits. However, the more difficult we can make it for the fakers, the less of a problem it would be.
Note: All my coins are in a safe deposit box. I keep nothing in my home.
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