Action pins are usually made out of low carbon steel. And then hardened. Simple fact is that over time, and depending on how the pins were initially fitted up, and even how good the threading dies and taps the craftsman was using when he made the pins, to how many times they’ve been loosened and then torqued down…they can wear out and start to over turn or go past their intended index point. You see this not only with breech pins, but on top lever pins, and cover plate pins.
As Steven has mentioned the breech pin out of index can be from a number of different causes, as can the hand pin. These two pins do more than just hold the stock onto the action. The breech pin actually bears on the wood and when tightened will draw the head of the stock tight into the action. That’s why that pin is normally tapered.
Nobody notices a hand pin that isn’t tightened down completely because its slot is hidden under the trigger guard tang in most instances. Take a few guns down to the bits and you’ll start to notice that hand pins are usually pretty loose. Tightening them down will draw the rear of the top strap further down and you’ll start to see the pin protrude from the top strap, which will need to be filed flush so the safety will work correctly and for aesthetics.

I don’t think I’ve ever heard of or seen a craftsman using spacers to correctly index a pin. Can you provide an example of this method (pics or vid)? I’d be interested in seeing the method.

Most craftsman will just make new pins to fit. I’m making a few right now. I just finished up making two new cross pins for a Greener FP.