Stoke attacker Jese went down what was deemed to be a push from Dale Stephens in the 91st minute and, were it not for Mat Ryan's heroics, would have cost the Seagulls dearly.
Hughton said: "My impression at the time is it was soft but you never really know until you come in and see it again. My view hasn't changed. What you've got if you've got is Dale Stephens and the lad Jese that are both, in effect, holding each other and if anything it almost looks like Dale is pushing him off him almost.
"When you see what goes in the box, not in an aggressive way, and hence yes I thought it was a real poor decision and a real soft soft penalty."
Charlie Adam's penalty was well saved by Brighton's Australian goalkeeper and, as Adam went to slot home the rebound, centrehalf Lewis Dunk made an excellent challenge to prevent the certain goal and clear the ball for a corner.
"The save was good but if anything the clearance was even better. It's not as if it's one of our quick players that are getting to that ball first and Lewis Dunk, who I thought was excellent today, had to make a real good challenge on that one otherwise it would have been close to being another penalty. If anything the save was good but the clearance was even better."
Hughton's men started brightly, going in 1-0 up at half time, but Stoke piled on the pressure in the second half to equalise and almost snatched victory.
"I think on the balance of play I thought we had the better chances, we were very good in that first half up against a Stoke side that I think have been good, really good in the last couple of games.
"They're obviously changing the way and pressing a lot harder and getting the ball forward a lot quicker but I thought we were good - particularly on the counterattack and over the 90 minutes had the better opportunities. I know they've missed a penalty but I thought in general play we had the better opportunities to score."