The hosts took the lead in Saturday's Premier League clash at Carrow Road via a Bradley Johnson header from Robert Snodgrass' corner on 56 minutes.
But Stoke equalised on 73 minutes when Jon Walters slotted home a penalty after substitute John Guidetti had been brought down by Sebastien Bassong in the box.
Walters was sent off soon afterwards for a high challenge on Alex Tettey but the Canaries could not make their numerical advantage tell as they were held to a draw which leaves them just four points above the drop zone.
Hughton agreed it was two points dropped, telling Sky Sports: "Very much so, and that's my feelings at the moment.
"We're up against a physically strong, direct team in Stoke that certainly caused us more problems in that first-half period than perhaps in the time when they gained the penalty.
"And at 1-0 up, I felt we dealt with everything that they had to throw at us in that second-half period and, as I said, it was probably the period of the game that we were more comfortable.
"But we've conceded what I think from the referee's point of view was a very, very soft penalty - some might be given, but certainly some wouldn't be given in that same exact situation.
"But we allowed ourselves to be in that situation, it was a longish throw that we needed to deal with better than what we did.
"So that's the frustration at the moment. It then becomes hard towards the end of the game when they go down to 10 men, because there's probably no team that are better and no team that are bigger and physically stronger to be able to deal with getting 10 men behind the ball so we found that one difficult.
"At this moment, it feels like two points lost because I felt we weren't fantastic today but I thought once we got the lead, I felt we were comfortable enough and (conceded the penalty in) probably the period of the game that we were most comfortable."