The champions were sunk by a second-half solo Mame Biram Diouf goal at the Etihad Stadium on Saturday, ending their previously perfect start to their title defence.
Speaking to Sky Sports afterwards, Pellegrini insisted he had anticipated a tight encounter, particularly after a goalless draw at the Britannia Stadium and a 1-0 home win in last season's league meetings with the Potters.
"We knew that we would have a tough game today, against a team that defends very well with 10 players behind the ball," said the Chilean.
"Last year was very similar to today - we were lucky to score one goal and win 1-0. Today, we didn’t create important chances to score. We had two or three, but we couldn’t do it.
"We started with the most creative players that we have in the team - with Yaya, Silva, Nasri, Jovetic and Aguero. Today, two things happened - first, that we are not very creative and second, Stoke did very well."
Pellegrini went on to explain that he always had fears that City might not be able to come through their opening assignments with maximum points, as they struggled to get up to speed.
"It was very important to finish the first three games with nine points, especially playing here at home, but I was very concerned about the start to the season," he added.
"Our squad is not 100% fit and I think in the second half today, we saw it. Three or four players can’t play with the same intensity for 90 minutes.
"We now have 15 days, it’s not the best to have an international break, but we must continue working and try and recover in a difficult week after that."
New signing Fernando had to limp off after 38 minutes and Pellegrini said: "He has a muscle problem in his groin. Tomorrow we will have more information."
And when pressed on the likelihood of any late ins and outs ahead of Monday night's transfer deadline, he responded gloomily: "I really don’t know in this moment. We have a lot of restrictions in the number of players and the amount of money we can spend, so it’s not easy."