Fulham put themselves on course to break their 13-month winless away streak just after the half hour when Clint Dempsey came back to haunt Hammers goalkeeper Robert Green with the Cottagers' opener.
A few moments earlier, Hughes was livid that Marriner did not award the away side a penalty after Eddie Johnson went down in the box under pressure from Lars Jacobsen.
Replays showed the West Ham full-back had clambered over the back of the American, leaving Hughes to reflect on what might have been had his side gone in at the break with a 2-0 lead.
"I am disappointed we didn't get the awarding of the penalty because at 2-0 going into half time it would have been difficult for them to come back," said Hughes, who saw his side denied victory thanks to Frederic Piquionne's second-half header.
"Eddie got in behind the defence and if there is any contact whatsoever then more often than not it is a penalty.
"Unfortunately for us for whatever reason it wasn't given. From our point of view it was clear, there was a coming together, a tangle of legs and a goalscoring opportunity was denied, so it should have been a penalty."