The two managers exchanged words at one point in the dugout zone during a tempestuous affair, which saw the Red Devils' perfect start to the season come to a halt.
Mourinho accused Stoke of playing defensive football at times and going direct too often, though he did also concede that a point apiece was the correct outcome.
In response to these claims, Hughes told reporters: "That's just an easy swipe at us really. 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."
Stoke are back in action next weekend with a league trip to Newcastle United, while United host Basel on Tuesday evening in the Champions League.