Catcher is the QB and calls the plays in the infield, Center Fielder is the QB and calls the plays in the outfield. These two positions should be very vocal, and call the plays. I would think in this situation (bases loaded with bunt) the catcher should have been calling "4, 4, 4!" leaving no doubt where the play was to be made. Infield = home, outfield = either 3rd or possibly home, or a cut throw to hold the runners. Of course, there is no substitute for kids who have played together for several years, and work/communicate well with each other.
The coach should pencil this into his notebook for a "point of emphasis" at the next practice.