Nicolas Jackson and Noni Madueke had a row over who would take a penalty kick during Monday's 6-0 win over Everton, with Madueke initially refusing to hand the ball over to Cole Palmer, who later scored from the spot.
"I explained my feelings and in the future it cannot happen like this," Pochettino told reporters on Friday.
"The message was clear and now we need to move on. They are clever and understand the situation... in another way it's good that a player wants to take responsibility for a penalty.
"But they need to respect discipline and the rules which are so important. The way they wanted to do things was in a very wrong way."
City played 120 minutes in the Champions League on Wednesday before losing to Real Madrid on penalties and Pochettino said that could benefit his side.
"We know very well, when you play 120 minutes in the Champions League, the effort is massive. And the emotional thing, it's always not easy to recover after you lose," he said.
"Of course it will be tough for them, like it will be for us. But we need to remember they have an unbelievable squad... they are showing in the last six-seven years how consistent they are playing under Pep's philosophy.
"They are, if not the best, one of the best teams in the world in the last five, six, seven years."
Chelsea could have midfielder Enzo Fernandez available after the Argentine returned to training on Friday.
