City were beaten 2-1, with Guardiola complaining about a failure to match Bournemouth's intensity on the day.
But he also said: “The players have made an incredible effort because there are players that are not in the best way and they made an incredible effort to be here.
“So Manu, Nathan were not in really good conditions. Until the last moment I didn’t know if Nathan could play and he said ‘I want to try, I want to try’.
“That’s why after 2-0, we decide to pull him because we need him for next Tuesday in Lisbon. That’s why. It is what it is.
“Sometimes there are seasons where this happens more than the other ones. We have to handle it, people come back and sooner or later the team will be back.”
On Kyle Walker, he said: “Kyle, 18 or 19 days and only one training session with us and today he was there.”