The incident occurred towards the end and after the final whistle of their 4-1 win on Friday night.
“These things happen," said Allegri.
“I had three players who needed to be substituted because they had cramp. There was a misunderstanding, but it's no issue, these things happen.
“Is Bonucci already studying to be a Coach? It may well something he does in future, even if he still has do much to learn."
There are now reports Bonucci will be fined for the outburst.