It is definately NOT a common Honda fault BUT a common mistake of people rebuilding the 500.
There is a hardened steel locating pin in the crankcase the locates the bearing via a blind hole in the machined steel piece that is the outer race, if not located correctly on assembly the pin is pushed into the case cracking a piece out of the casting(this bit is not totaly destroying) which alows the bearing to move, this can cause excessive wear on the bearing needles and, unfortunately, the gear shaft end that is the inner race.
The only proper fix is engine out, all side covers, points plate etc off and remove lower case.
You can them extract the pin, which is in top case, and carefully refit with a bit of epoxy in the hole to seal the damaged case==not too much or the pin will stick out too far, carefully inspect the shaft and bearing for wear, luckily there are lots of used gearboxes out there you can get bits from BUT Honda did modify the tooth profile on a couple of gears through the years so if you do go used fit both shafts with all the gears OR transfer all your gears to another shaft but use new cirlips.
NOTE CB 550 shafts and gears WILL NOT FIT.
Have you only recently got this bike? As i suspect its been apart not long ago.
The job is not difficult, hardest part is getting mounting bolts out if corroded and i have, when a lot younger and idiotic, lifted the 500 engine out and in on my own, easier if you remove sump and strainer, oil filter housing and top cover from cam cover.
If you need the proper Honda manual i can point you at a download or even send you a dvd for post cost from UK