Robert Lewandowski struck his 45th goal of the season to hand Die Roten a 2-1 win to advance to the final in Berlin.
But Muller admitted he was concerned with his side’s performance despite a sixth successive win since German football resumed.
“Frankfurt showed a lot of fatigue in the first half. We were fresher, we should have taken a bigger lead,” Muller said. “But we too were tired and fatigued after the last few weeks, unfortunately it was similar in the second half.
“We were unusually sloppy. Our pressing wasn’t deserving of our name. Our defenders did a good job.
“They stifled a lot, but in terms of our play, the final ball, we can be anything but satisfied. We stepped on the gas after the equaliser.”
After Danny Da Costa cancelled out Ivan Perisic’s opener, Lewandowski responded as Bayern edged ahead once more.
And Hansi Flick opted to focus on his side’s good run and praised his players for extending their impressive run.
“It was a cup match, our opponents pressed very well, we were reeling at times,” said the Bayern boss. ”But at the end of the day it was a deserved victory.
“We should have taken our chances and scored one or two more goals, the second half would have been different then. But I still have to pay my team a huge compliment.
“We’re on a great run, the players are doing a very, very good job, so we can accept the second half. The main thing was to advance after such a cup fight. It’s the step we wanted to take: toward the final in Berlin.”