The Hornets held the Premier League leaders to a goalless first-half, with only Raheem Sterling briefly testing Heurelho Gomes in goal.
However, Sterling and City found the breakthrough with the England international’s first goal for the side during the second period, with Fernandinho adding a late second as City made it four wins from four.
The defeat is Watford’s first since returning to the Premier League this season, and Flores, while disappointed, was philosophical afterwards.
“[I am] disappointed, of course, because whenever you prepare a team you prepare to win,” he told Sky Sports. “But it was very difficult to play against Manchester City today. They played really well, kept hold of the ball.
“Manchester City is an amazing team, and we are learning from this kind of experience for the future.
“The players are confident, the comments in the dressing room are that we are ready to go back for the next match.
“The start of the season was very difficult, playing away at Everton and now at Manchester City – at these games it’s very difficult to earn points.
“But we are confident with the future of the team because they are working really hard, and they are focused on their target.
“We conceded the goal very early in the second half – we didn’t have time to prepare for the second half in the way we expected,” he added.
“In the first half the feeling was that we were very good in defence. We defended a lot of similar chances very well, when Manchester City tried to cross.
“Sterling was playing like a striker at the start of the second half. Maybe the central defence were a little surprised because they didn’t react so quickly, but we will learn from these mistakes.”