Aguero’s absence from the squad sparked fears City’s record goal-scorer had aggravated the knee injury that had side-lined him for several months.
But the boss says it is nothing to worry about and that Kun is assessed on a daily basis as he continues to build his fitness.
"Sometimes it is just a reaction on the knee,” said Pep.
“It is swollen. Hopefully tomorrow he can come back to training. With Sergio, it is how he wakes up.
“He makes good training sessions, but then has niggles in his knee.
“Yesterday we decided not to select him. This morning he woke up with little problems in his knee and could not train.
“We know the injury he had is not easy for the recovery - we have to handle it as well as possible. When he is ready, he will play. “
On the 5-0 win over Burnley, Pep was asked if the five goals would ease the pressure on his forwards.
City had failed to score more than one goal in a Premier League game since late September, despite creating numerous chances in many of the games.
"It was important to come back with a victory in the Premier League,” he said.
“It is one more game. We play a lot of games so to play 90 minutes and maintain a good level is not easy, but there are always things to improve on.
“Of course, it helps us. It’s important for us to score goals and keep going.
“Especially for Riyad. Gabriel has to score, Sterling when he plays has to score goals.
“We have to score, that’s why they are here and play up front. The most Important thing now is we have almost 21 players fit; this is important.
“We have players who are tired who will need rest. But the guys who defend well and the guys who score, will play.
“It’s not about rotations - they will play more before they are tired.
“Now we are focused on Tuesday and our game against Porto.”