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Part of the problem is how tiny the margins of error are. This is why you can find so many people online who think their 9F is aligned perfectly...they haven't looked closely enough.
The other problem is that if you align your eyes, the second hand and one of the second markers, those things will not be aligned any more in only a couple of seconds. Its very hard to judge alignment. Even a perfectly aligned watch will appear to be unaligned for most of the minute cycle.
I totally get why you feel the way you do. I would have felt the same way in the past. The reality is your watch is probably functioning perfectly and to a level of accuracy that a mechanical movement could never achieve and its only bothering you because you're looking for it!
@Stonehedge I love the fact that I only find out about all that after I got the watch :-) I thought I did my research haha always the way. To be fair it is barely noticeable but I’m crazy and have the jewellers loupe 😬