Marriner, who wrongly sent off Kieran Gibbs in March when he mistook the Arsenal defender for Alex Oxlade-Chamberlain, came under the spotlight at the Britannia Stadium after awarding Ryan Shawcross a second yellow card for a foul on Danny Rose.
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"Ryan's travelling at speed, he's got the flight of the ball and he's trying to get there. Rose is a quick player, and he's got in front of him and toed it away. It's clearly a foul, but that's all it is," he told reporters.
"The referee played on initially, then brought it back and then deemed it worthy of a yellow card. Whether or not 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's a second yellow and to have a sending off for that is rather harsh on Ryan and ourselves.
"I've been involved in games with Andre Marriner for many years and he's a top referee. I thought his performance today was really poor and whether or not his confidence is a little bit shot because he's been involved in games where his decisions have been highlighted in the past, maybe his confidence is a little bit low and it's affecting his performance."
Hughes' mood wasn't improved when Rose escaped a red card for shoving Geoff Cameron soon after Shawcross' dismissal, and he called on Marriner to explain why the full-back was only shown a yellow card.
"He [Marriner] frustrated us on numerous occasions, not least with the decsion on Rose. He's used two hands, everyone knows it's straight red, but he gives a yellow card.
"I think that needs clarification and to give us some understanding as to why that's not a straight red when it should be."
Spurs boss Tim Sherwood, meanwhile, praised the performance of goalscorer Rose, though he called on the young defender to learn from the pushing incident as he had to be substituted before getting himself sent-off.
"He's a matchwinner for us today. I thought he was performing really well today and I didn't really want to bring him off the field but I had to diffuse the situation," he admitted.
"The crowd were so hyped up, and I thought I just had to get him off the field and get him to the dressing room.
"My heart was in my mouth, and he's still a young guy. He scored the winning goal today and he's smiling becuase we haven't been reduced to ten men.
"He can learn from it and it's a positive. We've come away unscathed with a clean sheet and Danny can learn from that. He made the referee make a decision and he shouldn't be putting himself in that situation."