Hughton's Brighton side conceded in the 90th minute, conceding a late goal from Sol Bamba.
Lewis Dunk headed the Seagulls in front inside six minutes at the Cardiff City Stadium but Callum Paterson's equaliser and Dale Stephens' straight red card swung the game in the hosts' favour.
"We're frustrated and angry because when you're down to 10 men for such a long period of time, you certainly warrant getting something out of the game," Hughton told 'Sky Sports'.
"There are two big decisions - the first one is the red card and I think that particular challenge can go anyway. What Dale [Stephens] has done is give the referee a decision to make.
"I've certainly seen worse with the studs showing very early. There's not great contact with the player - some referees wouldn't have given it, some would have done, and that bit I understand.
"What I find harder to understand is, particularly at that stage of the game, a linesman that's in the position he's in getting that one [Sol Bamba's goal] wrong.
"We've seen it on numerous occasions and he's in an offside position. That's the frustration and anger. For me it's a comfortable and easy decision to make," he added.