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 here 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."