Referee Graham Salisbury waved away Marlon Harewood's appeals after the striker had been felled in the box by substitute Jamie McCombe's clumsy 74th-minute challenge, much to the astonishment of the home side and a crowd of 43,326.
Hughton said: "For me, it was an absolute certain penalty. There are some penalties where you are not sure whether the referee is going to give it or not.
"I could have almost looked away because my first impression was just waiting for the referee to point to the spot."
City boss Gary Johnson admitted his side had perhaps had a lucky escape. He said: "I must admit, my heart was in my mouth at the time.
"The lads felt there was a bit of contact but from our point of view, maybe he was starting to go down early, we don't know. But he (Salisbury) was very brave with forty-odd thousand people screaming for a penalty, anyway."