Overworked official Madley gave 38 fouls - the most in any Premier League match this season - but missed a key one when Charlie Adam shoved Valon Behrami for the winning goal.
Even Adam admitted to Sky Sports: "I think it was a foul actually, I pushed him," after his header came back off a post and went in off Hornets goalkeeper Heurelho Gomes.
Mazzarri refused Hughes' handshake at the final whistle of a bad-tempered game in which his side collected five bookings - two of which resulted in Miguel Britos being sent off in the final minute.
And the Italian said: "I was very angry at that moment with the referee and the time he gave at the end.
"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."
Hughes was unimpressed after Mazzarri left him hanging on the touchline.
"I'm a little disappointed," he said
"It is something maybe the foreign managers don't always do and they need reminding it is something we do over here.
"Mind you, British managers are in a minority these days so maybe we shouldn't expect it.
"It was an emotional game and I think he was a bit emotional afterwards
He needed to be reminded, and I've shaken hands with him since."
Watford put in a lethargic display which was summed up when an injury to Younes Kaboul was followed by the ridiculous sight of substitute Christian Kabasele taking an age to get ready to come on, leaving his side playing with 10 men for almost five minutes.
There was a distinct air of farce about Stoke's goal as well.
From Xherdan Shaqiri's 29th-minute corner, Adam's downward header struck the foot of the far post and bounced along the goal-line, hitting Gomes on the knee and rolling into the net.
Hughes had been hit by injuries to Ryan Shawcross and Glenn Whelan as well as a suspension for Joe Allen, but his patched-up side were deserved winners.
"I thought we were good value at the end," he added.
"Charlie was excellent
He had to be more disciplined than we usually demand of him
Usually he has a defensive midfielder alongside him but he did not have that option.
"I'd have to see the goal again before I can say if it is right or not, but the key thing from our point of view is that it is a winning goal."
Source : PA