Gary Hooper gave Norwich a 13th minute lead at Carrow Road on Thursday, but there would be little else to cheer about for the hosts.
Pajtim Kasami equalised with a free-kick 20 minutes later and Scott Parker wrapped up the win for the visitors in the dying embers, but Hughton feels his team should have been given a spot kick in the second half.
Johan Elmander jumped up to reach a cross but was nudged in the back by Sascha Riether, which went unspotted by the officials, to Hughton's ire.
"By the letter of the law it's a penalty," he said.
"But I'm not entirely sure about referee's angle. It's certainly one many wouldn't give, but Johan is barged in the back, there's no doubt about that.
"Some are given, some are not. But by the letter of the law, it's a penalty."
Hughton was keen not to use the decision as an excuse for defeat, however, and was quick to highlight that his players did not capitalise on the chances they did carve out.
He added: "We didn't make the most of our opportunities. I am really disappointed not to come away with a result.
"It is a concern when you do not get the result you feel you deserved. We made some poor decisions and perhaps didn't create enough clear-cut chances as the home team, but I don't think it is a question of players not caring enough."
The former Newcastle United manager also admitted that Elmander's poor form in front of goal is a growing concern, but recognised that the on-loan forward is helping bring out the best in Hooper.
He explained: "Lack of goals for Johan Elmander is a concern as you want to be scoring goals throughout the team, but he does give us a work-rate off the front.
"It is hard to play with two strikers up the park these days. Elmander's role has helped enable Gary Hooper to get the goals he has in recent weeks."
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