Flitcroft watched Hornets wing-back Ikechi Anya run more than half the length of the field to score the pick of the goals after strikes from Troy Deeney, Marco Faraoni, Fernando Forestieri and Sean Murray put the visitors on course for victory at Oakwell.
Tykes striker Jason Scotland cancelled out Deeney's opener to briefly put the hosts level.
Flitcroft felt Deeney's seventh-minute finish should have been disallowed but had no complaints about the result.
"The first goal they score is a yard offside, the linesman's not done his job," he said.
"The goal that we scored, Jason Scotland's goal, was just, and you're one-all; you've got to hold firm against Watford at that point and that's what's disappointing.
"We've not defended the box which, as a defender, you're not just paid to do that, you're brought up to do that from seven, eight, nine years old.
"At times my lads are just going out to try and make do and that's not something I profess here.
"I want everybody who comes to the football club to improve their own position and their standing in football.
"We've been below our standards and against a Watford team you can't even get away with 10 per cent off.
"But today some players were 30, 40 per cent off the standards they've set. They've let the group down; they've certainly let the fans down, definitely.
"I want to design a football team that wins games. It's something I'm obsessed with and, at the minute, we're not doing that.
"There's surgery needed and we're going to make that surgery and see where that takes us."
Watford manager Gianfranco Zola was pleased with the clinical finishing of his side but felt there was still room for improvement.
"Winning a game like this is never easy so therefore you have to enjoy it," said Zola.
"We know that we haven't been perfect out there. We know that there are some things that need to be done better but in general we go home with a big smile on our face.
"The game went exactly where we wanted it to be.
"We know they were pushing, they were looking to get it back, to come back into the game and we knew that they were going to leave space behind. We just waited, they had their chances too, and then on the counter we took the opportunities and did very well.
"This year sometimes we've played good football but the question was whether we were going to be as sharp and clinical and effective scoring goals as we were last year and I think today is a good signal in that sense."