Both sides went into the New Year's Day encounter needing a boost following a poor run of form, with the Irons last win coming against Chelsea on December 1.
The home side were given an early opportunity to take command when referee Mark Clattenburg spotted a shirt pull by defender Ryan Bennett on Winston Reid, and Mark Noble converted the controversial penalty.
Although Norwich midfielder Robert Snodgrass rattled the woodwork with a free-kick, Joey O'Brien crashed home a second goal on 26 minutes, which proved enough to secure the Hammers a morale-boosting victory ahead of next weekend's FA Cup tie against Manchester United.
Russell Martin netted a well-taken volley for his third goal in two games during stoppage time, but it was scant consolation for Hughton.
Snodgrass later posted a Tweet claiming "the referee kills the game. £gamesgone" - and while accepting there was cause for a foul, Hughton felt the penalty award was soft, as well as highlighting other calls which went against the visitors.
"There is frustration with the big decisions, the key decisions in the game did not go in our favour," said Hughton, who confronted Clattenburg as he left the pitch at both half-time and following the full-time whistle.
"We accept Ryan Bennett had hold of the lad's shirt, but I also saw Reid's forearm in Ryan's chest. They are very close, he is not pulling Reid so he cannot get away, it is something you see game in and game out right throughout the country.
"On almost every occasion you do not see a penalty, particularly when it is so early in the game, so I was very surprised when he gave it.
"I also don't accept it was not a foul on Alex Tettey leading up to the second goal and certainly was a handball in the first half and then Harry Kane had a penalty claim, so we were on the wrong end of some poor decisions."