The Potters were given a huge opportunity to snatch all three points in the relegation showdown at the bet365 Stadium on Saturday afternoon, only for Charlie Adam to see his spot kick kept out by Mathew Ryan in added time.
Referee Robert Madley pointed to the spot after Dale Stephens pulled back Jese Rodriguez inside the box, though Hughton felt that contact was minimal and Adam should never have been given the chance to potentially win the game.
"At the time I thought it was soft, but I was not sure and presumed I would come in here and see something different," he told Sky Sports News after the match. "I still think it is incredibly soft - there are two players grappling each other and if anything Dale is almost pushing him off him.
"The lad goes down very, very easily and probably we feel a little bit of justice done with the save, which was a super save. And of course Lewis Dunk with some brilliant defending from that. We conceded a goal to a very good player in [Xherdan] Shaqiri who has that type of quality on his left foot.
"But I thought we were very good in that first half, it was very difficult though to sustain that for 90 minutes. But over 90 minutes, and even in that second half, I thought we had the better of the chances, we knew we were going to be under pressure at times, which we were, but we defended really well.
"But I do not think there is anybody who watched that game that would think we deserved anything less than a point. Testament to us as a team and a back four who were very resilient in what they do. And in [Eric Maxim] Choupo-Moting and Shaqiri, they have wonderful players who can come in off the flanks.
"And when you are bringing on [Sadio] Berahino, then you know it is going to be a tough second half. I thought we coped with things really well today and had to defend well."
Brighton are now unbeaten in three successive league games for the first time since November.