Wednesday's 3-1 Champions League win over Porto ended on a sour note as substitute Fernandinho limped off in the closing stages and the veteran Brazilian is expected to miss four to six weeks with a muscular problem.
Summer signing Nathan Ake was missing from the match squad with what Guardiola described as a niggle in his groin.
Aymeric Laporte and Kevin De Bruyne were due back in training on Thursday, but resources are stretched ahead of a week in which City will travel to West Ham, Marseille and Sheffield United before facing Olympiakos at home on November 3.
"On Thursday we'll start with Kevin and Laporte training again, but I don't know how they'll come back," Guardiola said.
"We get players back and others we lose. In three days we go to London (to play West Ham) and then to France to play Marseille (on Tuesday) and then Sheffield (on Saturday). It's so demanding."
With Ake out, Guardiola turned to Eric Garcia as the wantaway 19-year-old made his third appearance of the season, leaving John Stones to make do with a late substitute appearance after Fernandinho's injury.
Garcia is wanted by Barcelona and has said he will not sign a new contract with City before his existing deal expires in the summer, but Guardiola has not given up hope of him changing his mind.
"I know he wants to leave, but maybe we can seduce him to extend his contract with us," Guardiola said with a smile. "He is a guy who is so stable in many, many things and I'm so happy (with him)."
City were made to work hard for Wednesday's win, falling behind to Luis Diaz's strike in the 14th minute before a Sergio Aguero penalty, Ilkay Gundogan free-kick and Ferran Torres strike turned things around.
Gundogan's 65th-minute free-kick was the Germany midfielder's last contribution, with Torres and Phil Foden already waiting on the sidelines to replace him and Aguero.
"As for the fact Pep was about to substitute me, I'm glad he didn't," Gundogan said.
"I was actually quite sure he was going to take me off, but he maybe saw an opportunity for me and waited."
The 29-year-old admitted he does not regularly work on free-kicks but, having been felled by Fabio Vieira to earn the opportunity from a central position, he felt the chance was in his range.
"I have to admit, I don't practise free-kicks a lot, but there are certain distances that I feel comfortable from and, for me, this was the perfect range," he added.
Gundogan is among those to have already missed time for City this season and said he was not yet back at full speed after testing positive for Covid-19 a month ago.
"If I'm honest, we are struggling a little bit with injuries and to lose Fernandinho towards the end of the game is another blow," he said.
"There are others, of course, plus some who have just come back and I myself am not fully there yet after having Covid-19.
"We are in different kinds of moments fitness-wise and that's the challenge this season and I don't think it will end for a while."