"For 60-70 minutes we've come here to do a task but 20 seconds have cost us," he said.
"We kept them quiet and their fans on the low side. But the goal gave them the edge and the verve.
"With a bit more belief first half I felt we could have caused them more problems.
"The first half was evenly matched. Second half - we allowed them a foothold. We lacked belief and we could have driven forward more.
"The first goal is sloppiness on our part from a short corner and you can't give Charlie Austin an inch in this league.
"I'm disappointed we didn't grasp the nettle because we had good opportunities in their last third to be a bit more adventurous.
"We were comfy but you've got to see details through. You can afford to switch off for half a second."
Flitcroft revealed defender Peter Ramage has sustained a thigh knock and will be monitored over the next week.
The Barnsley boss also revealed he has 'irons in the fire' regarding a left-sided defender and players 'could move out' next week on loan.