Per MLBTR: However, Boston circumvented that limitation by “packaging” more premium prospects with lesser prospects; that is, paying $300K for multiple prospects that employ the same trainers/agents and then allowing the players’ representatives to divide the lion’s share of the collective sums to the top prospect of the bunch, with the lesser prospects receiving a smaller portion of the money.
Basically, they cheated the system to overpay certain prospects.
Ex. if they could only pay $300K for a prospect, they gave $600K to two prospects and had their trainers split it $500K to one prospect and $100K to the other prospect.