The 44-year-old says that although he accepts the decision made by referee Mazzoleni, he is of the opinion that the goal was incorrectly not given and should have counted
The Dutchman looked to have scored a perfectly-legitimate goal in the first-half if not for the linesman's flag, and despite the former Cagliari boss disagreeing with the outcome, he did not resort to bitterness towards the match officials, instead praising their opponent's resilience.
"The team played a good game, although we scored a valid goal that was cancelled out by the referee, but that's fine with me," Allegri told Sky Italia after the game.
"Then in the second-half, Fiorentina posed us some difficulties through [Manuel Pasqual], while the goalkeeper [Artur Boruc] pulled off two major stops."
Allegri then offered his own view of Milan's performance on the night and apologised to the club's supporters for failing to mastermind three more points, but was encouraged by Alexandre Pato's cameo display.
"The team did everything possible to win, but we didn't find a goal and we had given [away] little or nothing to Fiorentina," he continued. "I only thought about a win tonight, and the guys did well, but I'm sorry for not bringing home the three points.
"Pato? He came into the game without any problems and did very well for 25 minutes."
The coach finally switched his attentions to their forthcoming Champions League fixture against Barcelona, but insists that form is irrelevant when the giants lock horns at San Siro on Wednesday.
"Barcelona will be a different [type of] game. On Wednesday we start at zero, then we'll see," he concluded.
Milan move to second place in Serie A, on 21 points, but miss out on the chance to claim top-spot following Lazio's draw with Napoli.