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I was running into this same issue last night and couldn't find anything for it!
I did some investigating, and it turns out that the game was making duplicates of the leagues, and that was duplicating the players. To check, if you go to the "MLB" drop down at the top, you should see only one copy of each league (I was seeing two of each league).
It kept happening as I started new saves, and the best that I can figure out is that it's because I was "Applying Template" at the beginning of the save, and that was duplicating it. When I didn't do that, the issue went away. Not sure if it's helpful for you, but maybe there's an issue along this line that could help.
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