After dominating the first half, Norwich were left to rue failing to take what chances they did create as United substitute Danny Welbeck grabbed the only goal of the game just before the hour.
Norwich have now not won in four Premier League matches, and they have only scored twice in that spell.
And with other teams around them in the table also stumbling, Hughton was disappointed not to take advantage and extend the gap to the bottom three.
He felt, though, that his side had done enough to at least take something from the game.
"It is a massive disappointment, it's certainly a game we didn't deserve to lose," said the Norwich boss. "On the balance of play, I thought we were excellent in that first half.
"When you're having the best period in the game – which we were in the first half – you've got to try and capitalise on it and we didn't do that.
"I thought we were good in the second half as well. It's a fortunate goal for them, but when that falls to someone of Welbeck's quality you expect them to score.
"Over the 90 minutes, I thought we were the better team, but of course it is goals that win games."
