The Tykes were trailing 2-0 at the interval to goals from David Ngog and Jay Spearing but fought back after the restart with strikes by Tomasz Cywka and Chris O'Grady.
They were ultimately undone by Craig Dawson's 59th-minute striker but Flitcroft felt the damage had been done in the first half.
"I don't really do interesting games, I do wins," he said. "We've got to win football matches and we didn't do enough first half to win that football match.
"We waited, we delayed, we were on our back foot and to win a football match, to win a fight, you've got to be on your front foot.
"You've got to be throwing the punches, instead of taking them and first half we took too many punches.
"Second half: front foot, fighting, we showed guile, we showed bravery and we took a Bolton team on that couldn't cope with that dominance and we've only dominated them for 45 minutes. We haven't dominated them for the first half, which is disappointing."