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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.
Article continues below"From the referee's point of view it's a very soft goal," he said.
"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."
"(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."
