Lewis Dunk deflected Ashley Young's effort into his own net after the winger fired a half-clearance back on goal in the 66th minute.
But debate surrounded the referee's decision to give the corner in the first place after the ball appeared to come off Romelu Lukaku before running out of play.
Hughton felt the incident denied the visitors a merited point.
"Sometimes the margins can be that little bit of brilliance or that little bit of fortune and it very much was that," Hughton told the BBC.
"[The] two most disappointing things are we got into some good positions and we needed to make more of them, and the goal itself.
"My view at the time [was] it wasn't a corner. Having seen it again, it wasn't a corner.
"In a tight affair we were good value and I’m really disappointed not to come away with anything."
2 - Lewis Dunk is the first player in Premier League history to score an own goal versus both Man Utd and Man City in the same season. Slam.— OptaJoe (@OptaJoe) November 25, 2017
"We've played three of the big six. We've been in all three games and we haven't been humiliated in any of them," he said.
"That will go some way with confidence in the changing room."