The Rossoneri fielded a makeshift line-up in the Audi Cup opener in Munich, but were 5-0 down after just 36 minutes.
Allegri remarked: "Jherson Vergara does not know Italian football, so he has to work. This is a process we must go through and it can go through some ugly moments, but we must be physically and tactically ready for the Champions League.
"We are a team with seven or eight players under 20, so we mustn't get affected by paranoia after certain defeats. It was impossible in the circumstances to think of coming here and dominating Manchester City."