The Red Devils faced Juventus in Turin on Wednesday evening before travelling across Manchester to play the Premier League champions, but Mourinho did not get the result he wanted at the Etihad.
Goals from David Silva, Sergio Aguero and Ilkay Gundogan cancelled out Anthony Martial's penalty, causing United to lose further ground on the top four.
Speaking to Sky Sports after the game, Mourinho said: "I think it is not a bad performance at all. It was a performance with mistakes and we paid for it. All three goals are our mistakes. Against a team like City, if you make mistakes you will get punished.
"We had two matches away [Juventus and then City], it is not the physical effort but the mental pressure. I think some of the boys felt it a little bit.
"The first one is a bad one to concede and the second one is even worse. The third goal kills everything.
"Everybody has to agree. It is one thing to go to Juventus and play against one of the best teams in the world for 90 minutes. Another thing to beat Shakhtar Donetsk at home 6-0 and be very relaxed. We arrive in different circumstances.
"We cannot lose the ball the way we did. It is not about David de Gea, it is about the way we lost the ball."
United now sit eighth in the Premier League table, seven points behind Tottenham in fourth.
United will face Crystal Palace at Old Trafford after the international break while Pep Guardiola's team will travel to West Ham.