The Bundesliga champions were unable to break down their hosts at the Imtech Arena and the Spaniard was unhappy about his side's quality in the final third.
The official Bundesliga website quotes him as saying: "It was difficult settling into the game after playing Manchester City in the Champions League.
"We were a bit better in the second half, but unfortunately we didn't take our chances. We've got to carry on the work. It's going to be tough for us between now and December."
The draw leaves Guardiola's side fourth in the division.