Having taken the lead through Mame Biram Diouf, Stoke were pegged back after 41 minutes when Asmir Begovic was adjudged to have fouled Yannick Bolasie in the penalty area.
A frustrated Hughes felt Marriner interpreted the situation incorrectly and Stoke suffered as a result, Glenn Murray netting from the spot before Wilfried Zaha secured victory for Palace.
"My take on it [the Palace penalty] was that it's just a long ball," he said. "Maybe we haven't dealt with it but then you see the replay and you understand why because I thought the lad Bolasie has got his foot up high, I think it's above shoulder level.
"So that's what has taken the eye of Asmir, that's why he's missed the ball and the referee deems it a penalty, in my view it was a free-kick the other way for dangerous play.
"That was a key moment, those are the big decisions you want the referee to get, but Andre Marriner missed a lot of things."
And Marriner's decision not to penalise Joel Ward for a block to deny Diouf as Stoke pushed for an equaliser at the Britannia Stadium just added to Hughes' ire.
He added: "The second half [claim] was clear, arguably that was the best save of the match.
"[Palace goalkeeper Julian] Speroni's done great but it's a full-length save [from Ward], he's got two hands on it.
"How he doesn't give that is beyond me.
"On the day it just wasn't to be, but in comparison to my feelings following the game at West Brom [a 1-0 defeat last Saturday], in terms of a performance, I thought we were much, much better.
"In that regard I am reasonably happy.
"I'm obviously disappointed that we didn't win the game, just like everybody else connected to the club is, but for me it was just a case of not getting the breaks."
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