If it's a simulation issue, personally I would write a letter about the glitch to support, and they would probably fix it in the next patch. You most likely wouldn't be able to fix the issue manually.
The players in AAA and AA can wear the same numbers as someone in the majors. It’ll just change them when they are on the same team. You’re a Dodgers fan so for example other players can wear 17 like Ohtani but once in the majors it’ll change them. They can also wear retired numbers like 32 is retired for the Dodgers while they play in the minors but once called up it’ll change.
I preferred Franchise Mode in MLB 23. Except for the fact that MLB 23 would constantly freeze and unless you saved the game at different points you would lose the entire game you had reached in the game and start all over. This complaint was made over and over but no action was ever taken to correct this situation. Still I feel it is a much better game than MLB 24 and will continue to play 23 instead of MLB 24.