I've setup a fictional league starting in 1901 using the 16-team MLB structure with 4 levels of minors. I'm using historically accurate modifiers.
I'm not sure that this is a "bug," per se, but I do think it is something that can stand to be tweaked.
Take a look at this player (Stein Broomhead):
A very good hitter, with a great chance at 3000 hits.
In Spring Training of 1921 he gets a fractured skull, missing the entire season. That's okay, he's under contract with St. Louis for 2 more years. But for the 1922 season, he loses his starting OF job. Okay, he can still collect enough hits as the 4th outfielder. But look at his last 2 seasons. His rating hadn't taken a real big hit, but he wasn't even on the depth charts of those teams. He wasted away on the bench, became Angry, remained Extremely Popular, but finished 97 hits short of 3000.
I would think that as a player is getting close to a major milestone, there should be some incentive to put him in a role that would allow him to achieve that milestone.