After conceding the opener on 18 minutes to an outstanding Arsenal team move finished off by Jack Wilshere, the Canaries largely had the better of the game - only to fall further behind just before the hour mark to a Mesut Ozil header.
Again, they came back at their hosts and scored through Jonny Howson with 20 minutes remaining. However, their pursuit of an equaliser was in vain as Aaron Ramsey tricked his way through to score and Ozil netted again in the closing stages.
"I think the scoreline flatters Arsenal," said Hughton. "There's no doubt on the quality that they've got... when you look at the individual goals, in particular the first and of course Ramsey's, it's the type of goal that they can score.
"But I don't think it's a true reflection of what we saw today. We had some very good periods, particularly in that first half when I thought we were really unfortunate to go in at 1-0 down, but they have that type of quality.
"At 2-0, it looked like it was going to be a tough day for us but we managed to get ourselves back into the game and at that stage, we were very much in the ascendancy.
"But you make decisions then - do you have an opportunity to get a draw from the game? You have to go for it, and it leaves you vulnerable. Their quality picks you off in the end."
On the crucial second goal, Hughton added: "It was key for them and a blow for us.
"Fortunately, we were able to pick ourselves up and we showed some real intensity in the way we played, and some real quality. Getting back to 2-1, I thought we thoroughly deserved that. But in our endeavours to get back on level terms, we've left ourselves open."
The result leaves Norwich in the relegation zone with seven points from eight games, and Howson's strike was only their sixth in the Premier League thus far this season.
"What's concerning me is getting points and winning games," said the City boss, who handed a full Premier League debut to former Celtic ace Gary Hooper as Ricky van Wolfswinkel was missing with a toe injury.
"We've got to score goals ourselves. We're getting into the areas - and it's always going to be tough here.
"It was in effect Gary's first game, and he'll certainly get better with more."