The referee ruled differently and Aberdeen went on to be victorious after extra time and penalties.
"It might have been a different outcome because I felt we were denied a stonewall penalty with Richie Foran," Hughes said.
"It was a stonewaller, even from where I was in the dugout. You saw the reaction of my players, so that was disappointing.
"It is not sour grapes, I give all credit to Aberdeen and we rode our luck a bit when they hit the post but when it is a penalty, simple as that. It would have changed the game, I think we would have gone on to win it.
"But when it goes to penalty kicks it is anyone's match. I am disappointed for the boys but so proud of them. It could have been our day."
Hughes, though, dismissed an earlier Dons claim for a penalty when Adam Rooney went to ground after a challenge by Caley defender Josh Meekings.
He said: "That was a dive. But I am not having a go at the referee. I thought it was a good football match."
- Sports & Recreation
- Richie Foran
- Andrew Considine