Barcelona were only 1-0 up when the young Frenchman found the woodwork, but the hosts increased their lead just moments later.
They went on to collect a 4-0 win, enough to overturn the 2-0 first leg deficit.
"If the ball had gone in then the tie may have ended in a different manner," Bojan, who belongs to Barcelona, told Milan Channel.
"Barcelona are a great team, but they are human," he added. "I'm disappointed with how the game went.
"We were very happy with our display at San Siro and to come here with an advantage. We battled, but this is football."