In a crucial game in the fight to avoid relegation from the Premier League, Norwich were leading through Bradley Johnson's header until, 17 minutes from time, referee Andre Marriner awarded the visitors a spot-kick for Sebastien Bassong's foul on John Guidetti.
Jonathan Walters stepped up to convert his second penalty in as many weeks to earn his side a draw, before being sent off five minutes later for a high challenge on Alex Tettey.
Norwich saw two potentially vital points slip away with Marriner's decision, and Hughton was less than pleased afterwards.
"From the referee's point of view it's a very soft goal," he told reporters.
"There are certainly some referees who wouldn't give that. I think it's a soft one.
"It's a coming together, the lad's on his way down but I think there's no doubt in some circumstances referees wouldn't have given that so it's a soft one.
"But we shouldn't have allowed ourselves to get into that situation."
Despite playing the final 12 minutes a man to the good, the hosts struggled to break down their stubborn opponents, but Hughton felt they should have made the game safe before that point.
"When it was 11 v 11 we need to be better than we were either by getting the extra goal or by making sure we didn't concede," he said.
"Playing against 10 men is tougher, particularly against a side like Stoke.
"It becomes tougher because in effect they'll put a lot of bodies back behind the ball, and unless you're getting into the areas behind with real quality you end up getting the ball into the box and get a lot of shots from outside the box."