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Unless you use fictional players to fill them out, the minor leagues will be largely empty because the historical database does not include players that did not play in MLB during the season in question. I think that's the source of you're problem: you were thinking that all minor league players are also included in the game. That isn't the case.
If you use ghost players, they will fill out the minors so that games can be simmed even though there are only a few real life players that are assigned to the minors.
If you use fictional players in the minors but use the option to block them from reaching the majors, that's another option.
Of course, using the reserve list as opposed to minors is also another way to play. I often use the reserve list because I use recalc only, I don't use player development, and I don't really care about what happens at the minor league level.
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