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I would check the playoff roster options. While you can't necessarily change them during the season, I believe you should still be able to disable them. I was actually looking at this yesterday and I think if you're playing with no minors (ie. reserve roster only), and you have your playoff rosters set to use the "secondary" roster, the AI would not know which players are eligible and end up with a roster size 0, which sounds like your issue.
But if you disable the playoff rosters, then run the AI manager on all teams, I think that should resolve the problem.
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