The Sky Blues managed to come from behind to beat Porto in the Champions League on Wednesday.
But with a number of players sidelined after a short preseason, Gundogan says there is exhaustion in the dressing room.
"If I'm being honest we are struggling at the moment," the German said.
"Fernandinho went off at the end, we have players playing in different positions. I am not 100% there because I had Covid, we are not all at the same moment.
"That is the challenge for this season, it's not going to end for a while. It's not going to be difficult for Pep to pick an XI because players are going to be tired."