Johnson was not injured and shook his head as he left the left but after the controversy over substitutions in City's loss to Bayern Munich last month, Mancini insisted there were no more problems.
He said: "We didn't have many players in the middle and I wanted to move Yaya (Toure) behind Edin (Dzeko).
"Adam played very well but at that moment I had to do a tactical substitution.
"I spoke with him (afterwards) and he understood this.
"Sometimes every manager decides to make a substitution. Unfortunately some player has to leave the pitch.
"I understand any player leaving the pitch after 38 minutes would be disappointed but Adam is an important player for us."