This sort of thing generally only happens when you have roster limits set at the lower levels of the minors. It's not an issue with the basic game, it's an issue that certain specific settings can trigger though. To clear it up, it should be as simple as removing the roster limits in rookie ball.
Beyond that, this isn't the right place to post this sort of problem as the proper people to help with the issue aren't going to see it here.
You'll want to post it in a new thread the bug report forums. This thread is just for issues with the real player MLB/International roster set
