Flitcroft's men have been in fine form and came into the match on a six-game winning streak but this setback leaves them fourth from bottom, and just three points clear of their conquerors at Ashton Gate.
Flitcroft said: "I knew our great run had to end somewhere but the way it ended surprised me. The goals we conceded were very poor.
"We couldn't defend set-pieces and it is back to the training ground in that respect, and we couldn't handle City's strikers.
"Jon Stead and Steven Davies out-muscled us for most of the game but we will dust ourselves down and come again.
"I have an honest bunch of players and they showed great spirit after going 5-1 down, so I'm sure this will just prove an off-day.
"The way the run ended and the way we were dominated led me to some concerns but it's a case of trust now.
"We didn't get near them and we didn't compete but we'll put it right for an important game against Bolton."