Yannick Sagbo won the spot-kick that saw Hull score the only goal through Robbie Brady but minutes later was sent off after he clashed with Russell Martin.
It left the Tigers to play with 10 men for more than an hour but they held out for a deserved three points.
"It was a soft penalty - the lad was never going to get to the ball, it was going over his head. There is some contact but you see that in every game."
Hughton said his team had then failed to take advantage of having the extra man.
He added: "We certainly had enough possession but we came up against a very resilient Hull team and that can happen when they are down to 10 men. We needed to show more quality in the final third and with the final ball.
"This league is too unforgiving with too much quality and everyone is fighting - they were down to 10 men and fighting for their lives.
"For us it is a missed opportunity and apart from the penalty our keeper has really not had a save to make."
- Sports & Recreation
- Robbie Brady