Allegri wanted to do it gradually, though. Yesterday he said: "We had already tested this out (the 4-3-1-2) at the start of the season. To have a sense of consistency with these players and more guarantees, we kept the 3-5-2 and interpreted it differently so far"
He started with Conte's 3-5-2 and with Conte's interpretation of 3-5-2. And things went well. But during the transformation from 3-5-2 to 4-3-1-2 we had the most problems. The transformation was from Conte's 3-5-2 to a 3-5-2 with Pogba and Vidal/Marchisio playing much more wide than in Conte's system. This, lets call it Allegri's 3-5-2, brought bad results but was a needed phase between the 3-5-2 Conte used to play, and a 4 midfield formation, with Pogba and Marchisio playing wide.
Well, at least this is how I understood Allegri's statement. In the first month he kept the old formation, while in the second month he started transforming it into what he wants to use from the third month on.