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 he 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."