With regards to the grading, whilst it may be rim filing, the truth is that it is such a small amount of damage that I would not expect it to prevent the coin being graded.
As for the numbering, it almost certainly would not have been noticed when grading took place. This would be because A) it is faint, and B) because at sub choice for MS, there are expected to be dings and marks like this on coins - but they did not notice that it was deliberate damage.
So overall, yes it should NOT be MS62 because of the graffiti, however I can understand how it got through because the graffiti is very light indeed.
It should be noted that grading agencies often do make mistakes. but I do not believe that the rim issue would have compromised the grade even if noticed because it is too light to be obviously deliberate. Such damage could have come from sovereign money holders/clips etc. and given the limited damage it would usually be ignored for a low MS grade and considered part of regular bag mark type stuff.
As for the nails - check out this example from Heritage auctions.
https://coins.ha.com/itm/australia/...115-30004.s#this is EXACTLY the same as yours (although it is an AU example) and has the nails technically not attached to the hand
Different dies will have slightly different details especially from that period.
As for authenticity, the best thing to do would be to compare the dings etc to the photo from NGC that they took so that you can know if this is the coin that was graded.
To me this doesn't look suspicious as a fake however.
What I can say is that, it looks particularly nice for an MS62 despite the things you mentioned so it is likely that the grader looked at it and noted at least the rim damage and adjusted the grade slightly. I do not think the graffiti was noticed but it is very light indeed
Grading agencies DO make mistakes all the time, however this one is very marginal. if you notice it then sure, but I do think this coin will pass for something like MS62 generally. The graffiti is an issue but many people might not even regard it as being graffiti - it could have been due to an imprint from some other coin pressing against it in a money clip for example.
So whatever it is, its not THAT far off being a fair grade and it can arguably be the right grade. At this level of detail nuance is very important.
Finally, it should be noted that even an MS70 grading is technically ONLY flawless at 5X magnification. Any imperfections below that magnification would technically NOT affect a perfect grading.
Oh sorry and yes the deposits in the rim are totally standard and are bits of skin and dust deposited over time.
It should be noted that UNC doesn't actually mean it was never circulated as you cannot tell that. What it means is that their is no VISIBLE wear on the coin consistent with circulation. Those are two very different things. There is every reason to expect that this coin WAS circulated for a while before someone collected it but that doesn't in any way mean it is not MS.