The Rossoneri appeared to be in absolute control at the Stadio Franchi, but Adem Ljajic and David Pizarro penalties completed the comeback for a thrilling 2-2 draw.
“We controlled the first half well, but when going a man up we did not deal with the situation the right way,” Allegri told Sky Sport Italia.
“The second half were not positive, as we were caught napping. It’s a shame, as this could’ve been a very important victory to cut Fiorentina out of the race for third.
“We need to stay calm now, as we do some great things and the mistakes are part of the maturation process of this side.”
Nenad Tomovic was harshly sent off before the break for an elbow on Stephan El Shaarawy, though it appeared to be involuntary.
“Paradoxically, Milan played better against 11 men than 10,” confessed the Coach.
“It was difficult for the referee today, as decisions were taken in favour of and against both teams. At the end of the game we put everything back in the balance and that is a shame.
“We let ourselves go in terms of intensity and were half-asleep. We need to improve in terms of determination and effort.”
There was also a heavy blow, as a foolish Mario Balotelli booking for stopping a free kick from being taken quickly means he is suspended for next week’s clash with Napoli.