The game ended goalless at the KC Stadium after fine performances from both goalkeepers - Stoke's Asmir Begovic was impenetrable in the first half and Allan McGregor produced an even better display after the interval.
The only time the ball did cross the line, when Ireland tapped home from a yard after McGregor brilliantly denied Peter Crouch, the referee's assistant raised his flag.
Replays suggested it was a correct call by the narrowest of margins, leaving Hughes to reflect on what might have been.
The Welshman pondered whether his side might have been given the rub of the green in the officials' mind but could not deny the verdict was the correct one.
"It's very marginal...Stephen said it was (offside) by a shin pad's width and that's probably a good description of it," he said.
"It maybe was slightly offside, but sometimes you get them.
"You would like to think they'd give the benefit to the attacking team, the team who was trying to win the game, but having seen it on the video it was the correct decision."
The Potters, who lie just behind Hull in mid-table, have lost five of their eight away matches this term and Hughes was pleased with the way his side went about their business.
They were boosted by last weekend's 3-2 home win over Chelsea and Hughes was pleased to add another point to the tally.
"I thought for the vast majority of the game we were in control, certainly the last third of the match," he said.
"We looked like the team most likely to win the game in that period, we were really positive and had a number of clear-cut chances that, on another day, we would have converted.
"In terms of restricting Hull to any period of concerted pressure or momentum I thought we did that really well as the away team.
"I'm reasonably pleased with the away performance.
"Last time on the road we didn't have a great performance at Everton (a 4-0 defeat) but today it was important to build on the Chelsea result.
"The continuity of performance is important for us and that's one defeat in the last eight games for us.
"We're showing a good resilience to our play."