The Hornets were on the receiving end of their heaviest ever Premier League defeat when the champions inflicted upon them an 8-0 defeat at the Etihad Stadium on Saturday.
Flores, who is in his second spell as Watford manager, saw his side claw back a two-goal deficit against Arsenal at Vicarage Road last weekend but they went behind in the opening minute against Manchester City and never recovered.
Watford were already down by five goals by the time the clock hit the 20th minute mark before they shipped three more after the break.
Manchester City also put six unanswered goals past Watford in last season’s FA Cup final and that result looks rather respectable given Saturday’s mauling.
With Manchester City winning the last 12 meetings between the two sides and scoring 46 goals in that run, Flores admits his players are scared to play the champions.
"They have very bad memories playing against Manchester City," he told a news conference, in which he apologised on a number of occasions to the club's supporters.
"Before the game in the press conference one of you reminded me of the scores against City in the past years.
"It is like a prophecy that you are scared to play against Manchester City. Now we can try to forget them.
"We can think a lot about what happened in the match, but we lost in many ways. We conceded goals in many ways. It is our work as coaches to prepare much better for the next match."
