Guardiola did not reveal the extent of the injuries but was clearly concerned, with Saturday’s FA Cup semi-final against Liverpool to follow.
The Reds made seven changes from Sunday’s high-intensity 2-2 Premier League draw at City, as Jurgen Klopp rested a number of key players in their Champions League last-eight tie with Benfica on Wednesday.
But Guardiola made just two for the tough test against the Spanish champions.
“Today we celebrate because it is the third time in Manchester City’s history we are in the Champions League semi-finals,” the City boss told BT Sport.
“But we can’t forget we played three days ago, travelled, came here, have a lot of injuries now and I don’t know what will happen in the next weeks.
“We cannot play all the time and score four or five goals, we are human beings – we come from a difficult game against Liverpool.
“We are in big trouble.”
Wednesday’s second leg in Madrid was a bruising encounter all round for City, who had to contend with an Atletico side showing far greater ambition than in a first leg where they failed to have a single effort at goal.
Diego Simeone’s side were also extremely physical, allowing this to spill over into ill-discipline late on, with Felipe seeing red for a dangerous follow-through on Phil Foden, having earned his first yellow card for an elbow to the same player that drew blood.
The second yellow sparked an on-field confrontation between both sets of players and those on the two benches. Former City defender Stefan Savic appeared to headbutt Raheem Sterling and pull Jack Grealish’s hair in the melee.
There was also a suggestion Guardiola had liquid thrown at him as he headed for the tunnel, while there were reports of more clashes and police having to intervene.
“Everyone saw the action, but I have nothing to say,” added the City boss.
“It is the champion of Spain and they played with energy and, in the second half, were better than us and we were lucky we didn’t concede. In the first half we had chances, overall we are in the semi-finals – it is well deserved.
“The opponent is so tough, all the teams in the Champions League come here and suffer so it is important we go through.”
Saturday’s FA Cup semi-final with Liverpool is the latest in a crucial run of fixtures for City as they look to claim a Treble of domestic and European trophies.
Guardiola’s Premier League leaders and Jurgen Klopp’s second-placed Reds are separated by just one point with seven games remaining.
And both are now in the last four of the Champions league, with City looking to win the tournament for the first time – and on course for a final meeting with Liverpool, who face Villarreal in the other tie.