United lost today's derby 2-1, with all the goals coming before halftime.
"We were punished for many things," Mourinho told MUTV. "The first thing was our first-half. Our first-half.
"Some individuals just did not look fresh. Nor did the team. When you have three or four players not at the right level, you pay for that.
"The first 35 minutes we had City in control and deserving to be in front."
He continued: "The second 45 was very different. We fought very hard. We took many risks. I think we deserved a different result.