Sean Dyche was frustrated with the 94-second spell which ultimately cost his side one of the FA Cup shocks of the round.
Burnley led at half-time at the Etihad Stadium thanks to Ashley Barnes’ thumping strike after 25 minutes.
The Clarets frustrated all-conquering Manchester City - unbeaten domestically this season - but two Sergio Aguero goals in under two minutes just after the break changed the course of the tie, as Pep Guardiola’s side ran out 4-1 winners, with further strikes from Leroy Sane and Bernardo Silva.
Dyche said: “That can happen here, that was really my only overriding gripe with the team, because I thought we were very good up until their first goal.
“It was a bit of a contentious one, I spoke to the referee and he said he doesn’t have to blow the whistle, but I think when Ashley Westwood is five yards away motioning to say ‘are you going to blow the whistle?’ and he is the man who would be in the slot where they pass it to, I’m bound to be aggrieved.
“Sometimes in football, the rule might be the rule, but there’s a common sense moment, especially from experienced referees where they think ‘hang on, that’s the player that’s got to be in that slot, and I’ve just allowed it to be passed through there when he’s five yards away from the free kick, motioning towards me, are you going to blow the whistle?’
“But the next minute and a half was my biggest gripe. We looked a bit punch drunk, we didn’t clear our lines on two occasions, our shape went a little bit, and teams like this have the power to almost smell that moment, and then pick up their tempo.
“They did, and scored the second.
“Then we had to go for it, there’s no point, it’s the FA Cup.
“We made changes, we’ve got to protect the team at the minute with injuries, and once they’re in front, it’s difficult.”
Dyche and assistant Ian Woan had what looked a heated discussion with Guardiola after the first goal after a quickly-taken Ilkay Gundogan free kick, but Dyche laughed that off: “No, not really, you both fights you both want to win, you both want your teams to win, that’s just how it should be.
“Everyone is allowed to be passionate I believe!”
Both sides made four changes, fewer than anticipated after a hectic Festive schedule, and Dyche noted: “I don’t know their thinking, but it could be seen as a sign of respect, it could be a sign they definitely want to get the job done, either or, they won, and that’s their job.
“We put out a side we thought is probably as, at the moment, certainly the fittest and clearest side we can put out, and I was pretty pleased with it.”
And Dyche accepts the focus and concentration at places like this has to continue to develop to grow further: “I think there’s nothing they don’t know, you’ve just got to stay focused all the time.
“Especially against teams like this. It can be flat, it can be quiet, and then three, four passes, three, four movements, and suddenly it’s a goal.
“The higher up our learning, it’s that constant concentration and focus.
“It’s improved considerably.
“But the biggest thing though, we’re at the end of our squad at the moment, but the mentality...you’d never have smelt that.
“56 minutes in, you’d have been looking at our team thinking ‘that’s a team that plays together, that knows how they play, that are organised.
“That’s really pleasing for me and my coaches.
“When your team is at its most stretched, and yet they are operating how a team should, or how I think it should look, so I’m very pleased with that.
“You’re not going to come to places like this every week. We’ve still got some of the big super powers to play, but our mentality is growing, not just our performances.”
James Tarkowski wasn’t in the 18 after picking up an injury in training: “Tarky just picked up a niggly groin injury on Friday, we can’t risk anyone at the moment. We’ve got people off partly because we’ve got to try and have a go, but partly because we’ve got to be careful and protect people.”