City boss Phil Parkinson blamed a 15-minute spell after half-time for the defeat against Rotherham that means the Bantams are still only a point above the drop zone.
Chris Mitchell had levelled before the break but Rotherham struck twice in a six-minute spell to leave the home side reeling.
The City chief admitted: “We responded terrifically well to going a goal down but sometimes in football one response isn’t enough.
“We looked flat and for 15 to 20 minutes we didn’t cope well with Rotherham defensively. In recent weeks we have looked a strong side in that department.
“If we’d got through that period, I’m confident we’d have gone on to win the game but we got severely punished.”
Flynn pegged one back with a penalty in added time but saw his second comfortably kept out by Conrad Logan.
Parkinson added: “The keeper will get all the plaudits but Flynny normally strikes it a lot cleaner than that.
“It was a low dressing room. If that penalty goes in, everything is totally different but we’ve got to look at ourselves as well.”
Ricky Ravenhill made his debut in midfield after Ritchie Jones was ruled out with a damaged toe.
Simon Ramsden was also missing after complaining of a tight groin in training. The right back only recently returned from nine months out but Parkinson insists it is nothing to worry about.
“Simon felt a slight problem and sometimes you get that when you come back. Bearing in mind what he’s had in the past, he’s not the type of player we want to throw out there if he’s not right.
“Ritchie couldn’t get his boot on Friday. We had the option of giving him a jab to play but the doctor wasn’t 100 per cent convinced that would do the trick.”
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