Glenn Whelan was ejected in the 40th minute for two apparently bookable offences before Marc Wilson was given his marching orders for fouling Loic Remy in the area with referee Martin Atkinson awarding a penalty.
After the match, Hughes felt aggrieved by the calls and suggested his side could have won the game if they went in at half-time 1-0 up with a full eleven to play the second half.
"Apparently, he said that Whelan kicked the ball away, which bemuses me as (Yohan) Cabaye went over the top and Glenn reacted," he told Sky Sports of the Whelan red.
"Two minutes later he receives the second. An experienced referee should get the two players together and tell them to calm down.
"I'm dismayed by his performance. When you're on a yellow card you have to be careful, but Glenn's just as bemused as everybody."
Of Wilson's, he added: "I'm assuming it's for denying a goalscoring opportunity. My view is that there's a lot of pushing and pulling.
"He went down very easily, but nobody seemed surprised when the penalty was given."
Hughes added further: "We played really well, and could have scored more.
"Newcastle were struggling to stay in the game and keep up with us, before the referee made some decisions which changed the course of the game to our detriment."
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