Fer struck the ball into an empty net in the dying moments of the match rather than returning it to Cardiff goalkeeper David Marshall, who had put it out to allow treatment to be given to Alexander Tettey.
Referee Mike Oliver disallowed the goal and the Dutchman was heavily criticised for his actions in some quarters but, while admitting he has "dealt with" the situation, Hughton defended his player.
"He's been made aware,” the Canaries boss told reporters. “It has been spoken about, and for us it's something we left as soon as we left the changing room. It's been dealt with.
"Leroy spoke very honestly after the game. He's an honest lad. I think he just got caught up in the moment.
"It was a fairly frustrating day for us. It was a game we should've won and could've won reasonably comfortably.
"He's a very honest individual, but I think he just got caught up in the moment."
Fer joined Norwich in the summer from Dutch giants Twente, and has since missed just one of the Canaries' opening nine Premier League fixtures.