This is one part of the CBA which needs addressing next time around.

Ultimately, if amateur spending caps are deemed necessary by Major League Baseball and the players’ union, Boras would propose a hybrid solution – applying those limits only after the second round. That way, a team losing its top pick could apply its first-round budget to a second-round selection. Part of the reason to do that, Boras said, is to ensure that teams maintain or strengthen their current amateur scouting staffs. ...