Hughton's men slipped to their fourth defeat in five Premier League games despite a determined display, as they were undone by an Arsenal team in blistering form.
Jack Wilshere and Mesut Ozil put Arsene Wenger's side in command, and they made sure of the points with an Aaron Ramsey strike and a second from Ozil after Jonny Howson had reduced the deficit.
Hughton felt the scoreline was harsh on his team, although he accepted that a gap in quality had been the difference.
"I think the scoreline flatters Arsenal," Hughton said. "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. 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."
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