rogmax11,
I was seeing exactly what you described, so I started a thread a while back called "Deleted Retired Player = Recycled ID?" here:
http://www.ootpdevelopments.com/boar...d.php?t=130513
Markus got on a couple of times to confirm what you are saying, and what Comedian2004 says is the probable cause. If you have that setting on, the game recycles retired player ID's for those players who never made it to the "major leagues" (see what I posted there for my theory on what those are for this purpose).
FYI, this is not viewed as a bug, but as a tradeoff option. Apparently, if you have thousands of minor league players that never get deleted and recycled, the player history files get larger and more numerous, taking up file space and slowing the game down.
I feel (or have felt) your pain; this is why we need this option explained in an updated manual.