Steve Magadinno wanted DiGregorio to have the consigliere spot and was upset when Bonanno put DiGregorio on the shelf for not coming in when he was called (in his autobiography, Bonanno chalks Magaddino's support of DiGregorio to the belief that he could control him in the same way he controlled Nicolo Schiro in the 1920s). DiGregorio was then put under the protection of the Commission and became their first choice to replace Bonanno. (Magaddino may have also been the chairman of the Commission at this time).
That was one of the contributing factors in Bonano falling out of favour with the Commission, along with Bonanno's expansion into Montreal and Arizona, his attempt to send Bill and 40 men to California to kill Frank DeSimone and take over the LA family, putting Magliocco up to kill Gambino and Luchese, and then not coming in when the Commission called him.