Wilfried Bony led the charge with two goals as the Swans fought back from two goals down to lead with four minutes remaining at the Liberty Stadium.
"Given our history, in recent terms, we don't usually get them," Hughes told Sky Sports News. "Listen, we take the break, there was contact.
"I think Steven [Nzonzi] tried to flick the ball on, he was right close to the goal, and who's to say that if the lad hadn't got in the way, it might have gone in anyway?
"So I can understand Swansea being a little bit aggrieved but we've had situations like that ourselves."
A point helps Stoke stay out of the relegation zone.