The Spain international's free-kick seven minutes from time earned the hosts back-to-back Premier League wins as Watford were left to rue missed opportunities, especially in the first half.
Odion Ighalo wasted a host of chances while Sebastian Prodl was unfortunate not to be given a penalty after being hauled down by Matteo Darmian at a corner prior to Mata's winner.
"It's difficult from the bench to see what happened exactly - I don't like to protest," Flores told Sky Sports of Mike Jones' decision. "They can make mistakes but we have a very good level of referees in England."
Flores worked with Mata while at Valencia and felt his compatriot's quality decided a contest Watford should perhaps have taken something from.
"He's an amazing player, I know him from Valencia and we know how he takes free-kicks," Flores added.
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"He's very dangerous, it was a perfect place for him and he decided the match. I think we lost a very good opportunity to add some points and win at this amazing stadium.
"We played very well, kept the block very high, created chances but players with high quality, in one second, can change the match.
"We created gaps in their defence when they tried to build play, finally we played the way we wanted to play before.
"We came close to a good result but we were a bit unlucky. That's football and we have to accept the result."