If a certified coin is toned in the holder- was that the way it looked when it was graded- how would one know?

I bought my first MS Morgan dollar for my 20th century type set. It is a common date 1900 O- NGC MS 64. There is small dark spot on the reverse that is almost black. The rest of the coin has some light red-brown toning just around the rim, but nothing like this. I saw this spot in the auction and thought it might have been on the holder- I really did not know what it was. I got the coin lower than FMV -$75 out the door. Now I am thinking this spot is why I got it cheap. I see a lot Morgan collectors out there- have you ever come across something like this? Could this have happened after if it was graded or was it graded that way? I hope that the picture will show enough detail to form an opinion. Thanks! Happy Collecting!

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