Marriner was the referee who mistakenly sent off Kieran Gibbs instead of Alex Oxlade-Chamberlain in Arsenal's 6-0 defeat by Chelsea last month.
Hughes' main gripe was Marriner's decision to show Ryan Shawcross a second yellow card seven minutes into the second half of the 1-0 defeat at the Britannia Stadium.
Shawcross saw red after catching Danny Rose, who scored the only goal of the game with a header in the 33rd minute.
The Stoke fans felt Rose had exaggerated the foul and targeted him until he was substituted in the 69th minute shortly after picking up a yellow card himself for shoving Geoff Cameron in the chest.
Hughes said: "It's clearly a foul but that's all it is
"The referee played on for about five or 10 seconds and then brought it back and deemed it worthy of a yellow card, so whether he'd forgotten he'd already booked him, which for a senior referee is a little bit poor
"He should have had time to realise it was a second yellow, and to have a second yellow for that I think is rather harsh on Ryan and ourselves
"I've been involved in games with Andre Marriner for many seasons and he's a top referee
Today I thought his performance was really poor
"Whether or not his confidence is a little bit shot because he's been involved in games that have highlighted some of his decisions in the past
Maybe it's affecting his performance because h e frustrated us on numerous occasions
"Not least Danny Rose, who raises two hands
Everybody knows it's a clear straight red and he gives a yellow card."
Another contentious moment came early in the game when Shawcross felt Emmanuel Adebayor should have been punished for catching him in the face with an arm
"He was down for a good two minutes so something's happened," said Hughes.
"The referee missed that as well
Whether or not that was deliberate, I'm not sure
We felt aggrieved about that decision as well.
"But the top and bottom of it is we put in a fantastic performance
Under difficult circumstances I thought we were absolutely magnificent to a man, and the crowd responded to what they were seeing on the pitch.
"They understood we needed their backing and they were delighted with what they saw
The sound in the stadium was something special and I was really proud of everybody connected with Stoke City today."
Rose's goal was his first in the Premier League this season and his first for Tottenham since his stunning winner against Arsenal four years ago.
Tottenham boss Tim Sherwood admitted he feared the worst when the 23-year-old pushed Cameron, saying: " My heart was in my mouth
"He's the match-winner for us today
I thought he was performing really well and I didn't really want to bring him off but I had to defuse the situation
"I've never heard a crowd so hyped up
I thought I had to get him off and send him to the dressing room - out of sight, out of mind
"He's still a young guy, he's still learning his trade
We're smiling because we haven't been reduced to 10 men and he can learn from it.
"It is a positive because we've come away unscathed
We've got a clean sheet and Danny will grow from that.
"He did make the referee make a decision and he shouldn't really be putting himself in that situation
I've told him."
Sherwood disagreed with Hughes over the Shawcross sending off, adding: " I like tackling, I don't want anyone to get sent off, but it's two bookings."
Source : PA
Source: PA