Pato has conceded there's tension between the pair.
But Allegri has maintained that the working rapport between the two of them is just fine.
"There is no problem between Pato and myself," the former Cagliari man said. "The boy's outburst was just down to a moment of frustration.
"You can't always start every game, but this is not a serious issue and these things do happen from time to time.
"There are no problems and there wasn't a clear-the-air talk between us because there was no need for a discussion.
"He is training hard and isn't giving any signs of unhappiness."