Milan defeated the second-tier outfit with two goals in extra time following a 1-1 draw after 90 minutes.
"There are no easy victories as every match is played on the field," he told reporters. "I didn't expect to play extra time as I was convinced we would win. I wanted to keep the likes of [Carlos] Bacca and [M'Baye] Niang on the bench but in the end I needed them.
"When [Giacomo] Bonaventura, Niang and [Riccardo] Montolivo came on we improved in terms of quality. Some the players that started did well while others didn't, but that was to be expected as they rarely play.
"Along with that, Crotone showed they are a difficult team to play against and they had the backing of the many fans that came to San Siro."
Luiz Adriano, Bonaventura and Niang were on target for Milan as they secured their spot in the last-16 of the competition.