My understanding is this. There are middleman (not paid by MLB?) that promise delivery of players for such and such amount. The skimming is done by them, and families have no conception of what is going on. Those under investigation didn't necessarily take money, but aware of the practice. This caused the bonus amounts to rise steadily and smaller market teams with smaller budgets to feel left out. Did someone rat on someone?
One of the reasons why the milb chose to implement a draft system here years ago.
I am not sure if all the facts above are correct, but that was my understanding of what has ben going on down in the latin american countries.