Sir Alex Ferguson's men broke the deadlock through Shinji Kagawa on the stroke of half-time but it was his 76th minute strike that Hughton feels ended the contest.
Kagawa completed his hat-trick late on before a last-gasp Wayne Rooney strike sealed the win for the Premier League leaders.
Hughton believes Norwich were still in it up until the hosts' second strike of the afternoon after a dogged first-half display.
"The first goal yes, of course, hurt us, but the second goal hurt us more," he told Sky Sports.
"Of course you have to defend well against Manchester United but I thought we were a reasonable threat on the break. We perhaps could have kept the ball a little bit better.
"But I think the second one is the one that hurt us because at that stage you've got to open up a little bit to get yourselves back in the game and of course doing that allows United, with the quality they've got, to get into the spaces that really hurt us."
Norwich rarely troubled United goalkeeper David De Gea and Hughton added: "I think you always want to be a threat but we have to realistic coming to Old Trafford. You need to stay in the game for as long as you can.
"There aren't too many teams in the stature of ourselves who are going to come here and have lots of chances."