Eric Maxim Choupo-Moting scored a goal in each half as Hughes' men ended United's 100 per cent record in the Premier League this season by earning a 2-2 draw at bet365 stadium on Sunday (AEST).
It was a tempestuous affair on the touchline, with Hughes shoving Mourinho away from his technical area during the second half, before the Portuguese left the dugout at full-time without offering a handshake.
Speaking to reporters afterwards, Mourinho bemoaned Stoke's tactics as defensive – despite them becoming the first team to breach his backline this term – and claimed the match was "a game for [Marouane] Fellaini", given the willingness of United's opponents to take the aerial route.
But Hughes, who selected former Bayern Munich winger Xherdan Shaqiri and ex-Real Madrid forward Jese Rodriguez alongside Choupo-Moting in a creative front three, believes such claims are a hangover from Stoke's days of deploying Rory Delap long throw-ins under Tony Pulis – a style he insists his crop are far removed from.
"That's just an easy swipe at us really," Hughes said.
"You could argue United played more long balls, and why wouldn't they? They've got power and pace and if they can get those players ahead of the ball with good accuracy, they've got pace and power to burn.
"So I don't know what the stats are, but I'd argue that in general play they played more long balls than we did because they've got that threat and that's what they try to exploit.
"I think it's a bit lazy of people to keep on reverting to that 'Stoke are a physical team' thing.
"Goodness knows, we had too many free-kicks against us, but that wasn't because we're a physical team, it was because the referee misinterpreted too many things in my view.
"Overall we have changed, we're a different type of team. I try to bring good players here and we try to play football and I think you saw evidence of that."
Mourinho refused to be drawn on the altercation with Hughes and his decision not to shake hands at the end of the game.
"I don't speak about stupid things, I'm too old for that. Talking about stupid things is for stupid people," he said.