The Hornets slumped to a 1-0 loss at home to the Potters on Sunday but Mazzarri felt the only goal of the game should not have stood due to a foul in the build-up.
Mazzarri felt referee Bobby Madley should have called Stoke's Charlie Adam shoved Valon Behrami for the winning goal, which went down as an Heurelho Gomes own-goal.
The Hornets boss failed to shake hands with opposite number Mark Hughes after the match but revealed he did privately after he had left the pitch and claims his anger at the officials was to blame.
"I was very angry at that moment with the referee and the time he gave at the end," he said, as reported by ESPN. "I went into the dressing room and gave Mark my hand. I forget in that moment.
"But I was angry with the referee for not giving a lot of time and the decisions he gave. You have to look at the whole game; the fouls, the goal they scored and the yellow cards.
"Anyone can have a bad day. And this time he had a bad day."
Watford last week