The Latics caused City all sorts of problems for an hour but goals from Mario Balotelli and James Milner gave the champions the points.
Martinez was pleased with their defensive harrying of City, but going forward he felt his team lacked self-confidence in attack and he said that battling defeats are no longer good enough for Wigan.
"From our point of view, I think we edged the game for 60 minutes," he said.
"The disappointment is we couldn't get the first goal in that period. When you are just slightly ahead of the opposition you have to score and Arouna Kone had a clear chance.
"We could have been more patient but the frustration is we couldn't find a goal. That was the only thing missing.
"But I loved the attitude, effort and personality that we showed. We kept showing that desire. It was a very pleasing performance from many aspects but we are still disappointed.
"I don't want to be a Wigan Athletic representative saying we are happy to lose with a good performance against the champions. That is not accepted anymore.
"It is not good enough for us. We are disappointed we couldn't get a positive result. The performance off the ball was magnificent. The organisation was strong and for 60 minutes we were in the game.
"The disappointment is that we weren't ourselves on the ball and couldn't express ourselves. The lesson for us is that we need to be ourselves."