Manufacturing tolerances are generally well documented. One of the on-going problems is that operators and machinists are more and more being tasked as the last line of quality. No more line checks, no first article checks, no more Quality Assurance checks. (Cost Down savings) The parts go strait from the machine shop to the assembly dept. Your swing arm was 1mm off. On a metric travel indicator, which would be typically used with a Go/No Go function gauge to measure the swing arm, that represents one revolution of the gauge. That is an easy thing to miss, because the machinist or operator is looking for much smaller deviations. The gauge would show the indicator in the correct tolerance, but one revolution off.
Sadly, not every operator or machinist is as quality conscious as the next. Some will toss a known bad part in the bin with the rest of the good parts, just to show they made their production quota for the shift and avoid repercussions due to generating scrap. Sometimes things simply get missed too.
On the assembly side, if it goes together, no one is likely to notice a problem. High demands on product getting out the door sometimes mean people will accept out of tolerance or known sub-standard parts/assemblies in order to meet the immediate demands, letting Customer Service take the hit later. The Engineers often refer to this as "This Time Only" As in they know it's out of tolerance, but will let it go thru "this time". In reality, "this time only" becomes the new, sloppy, out of tolerance, standard and sadly more poor quality parts can slip thru the system.
Time and distance make it difficult for Yamaha to inspect everything they might want to when a problem like this occurs. Kudos to them for swapping the entire final drive. That the problem continues to exist would point to a new direction.