The Canaries led at the Emirates with five minutes remaining, with Michael Turner's header seemingly set to hand them a welcome win in their battle to steer clear of relegation trouble.
They were, however, to see momentum swing against them with the award of a controversial spot-kick.
Referee Mike Jones decided against taking action as Kei Kamara tugged Olivier Giroud inside the box, but his assistant called for a penalty and Arsenal would go on to net three times in the closing stages to snatch the spoils.
A disgruntled Hughton told Sky Sports afterwards: "The linesman gives the penalty from 50 yards. You have a referee who is 10 yards away who chose not to give it.
"What Kei Kamara has certainly done is end up playing the ball. Yes, of course, there is a little bit of contact, but I think the contact is maybe a little bit both ways.
"Sometimes you get an indication by the response of the players. Nobody appealed from them. The referee was 10 yards away and the linesman gives it from 45-50 yards away. I find that incredible.
"The same linesman on the third goal is offside, but he is 10 yards away and doesn't see.
"I thought we were excellent today, really. I couldn't fault the attitude and the aptitude of our players.
"When you come to somewhere like the Emirates, where you know it's going to be tough and you know you are not going to get the bulk of position and for 85 minutes you have given a really good account of yourselves, it's incredibly frustrating and disappointing when a decision is given by a linesman from 45-50 yards away."
Hughton added: "There is no doubt that he is holding him a touch, but I think it's both way. If he is holding them fair enough. But it wasn't the referee who gave it, so that is almost immaterial. The referee has a feel for the moment, he is the closest one, he must certainly have a better feel than the linesman does from that distance.
"I was incredibly surprised. I was surprised because nobody appealed for it. They had the momentum in the game.
"We are also questioning whether it was a corner in the first place. Normally when you have got a player that is seeing the ball out and he has been swept from under, generally it is a goal kick or there is a free-kick given. But the momentum of the game, it seems that something might have been given for them."