But CEO and general manager Marotta is adamant the relationship between coach and player was not the reason for Bonucci's shock exit.
"I want to point out that Bonucci did not leave because of Allegri," Marotta said in an interview with Il Giornale.
"He was not the cause. We were already prepared, because in the discussions a club normally has with its players, Bonucci had expressed dissatisfaction."
While Marotta was not surprised by Bonucci's departure, he was taken aback by Alves' transfer.
"Dani Alves was the real surprise, that was a bolt from the blue. He made a choice that seemed to be for Manchester City, then PSG turned up," Marotta added.
"There was a moment where we clashed, because I wanted the professional to show respect towards Juventus."
Juve paid €90 million for Gonzalo Higuain in July last year but made no such outlay in this past transfer window, with Marotta saying: "With Gonzalo Higuain, we had an opportunity during an historic moment as he left Napoli and we considered it a suitable investment, but you can't be expected to spend €90-100m every summer.
"The truth is, we defined the Higuain deal before selling Paul Pogba to Manchester United, although obviously that move was predictable and it facilitated our bid for Pipita."
Juve have won six successive Serie A titles and Marotta said it would be "a defeat" if they did not make it seven in a row. Leaders Napoli are a point ahead of Juve after 12 games with Inter, Lazio and Roma also in the mix.
The Turin club have also been beaten in the Champions League final in two of the last three seasons and Marotta said: "The Champions League depends on many factors. We were eliminated in Istanbul with Galatasaray [in 2013] because it snowed. In any case, in recent years I maintain the best team won in the end.
"My journey with Juventus is not finished and there is this challenge that we want to win the Champions League. Even after that, I don't see myself at another club. When [chairman Andrea] Agnelli wants me to go, I see myself working with the [Italian Football] Federation."