Would need to know the league setup to know what to look at further. But digging through the logic, if you are playing with ghost players enabled, then I believe we do tend to skip a lot of the minor leagues checks for valid rosters.
If you are not playing with ghost players enabled, then any game for the minor league teams should fail to run with an error saying that you are over the roster limits. I've checked and that functionality still does work for some test leagues I have.
Otherwise, please do feel free to upload your files (
https://support.ootpdevelopments.com...p-developments) and we can investigate further what might be the cause.