may need comissioner mode on for this suggestion:
go to that team's roster and transaction screen. under available actions select something that resembles "have ai setup complete minor league system". this can fix the problem often but not 100% of the time.
i use this before filling to avoid fictionally created players outside normal means. these players are mostly junk, no worries on balance isues, but occasionally a good prospect gets spit out too.
if the same team pops up a 2nd time with that same issue, i will use a team fill function at the lowest possible rung.
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real problem: not enough players created each year for your league structure. fill the teams with problems. slowly increase # of created palyers/year (more than 1 choice: draft, discoveries, iafa, etc) make 1 or more teams are not dipping in numbers below ~25+ at each level. more than 25 is probably better. the ai may bunch them up a bit.
if some teams have 4 rookie teams and others have 2, some teams will simply have nearly 2x what they need. rounds of draft and # of players created each year need to be enough to fullfill the needs of the largest system.
create more players and never have to do this again
