The hosts took the lead after 17 minutes when Peter Crouch pounced on Peter Odemwingie's rebounded effort to tuck home, but Chico Flores levelled things up just after the break.
Swansea were arguably the better side for much of the game and could have snatched a winner midway through the second half when Wilfried Bony was denied by Ryan Shawcross' excellent clearance off the line.
And Hughes conceded that it was hardly a vintage display from his side.
"Performance-wise it wasn't one of our better games to be fair, I think we're honest enough to say that but that's credit to Swansea and the way they played," the Stoke manager said.
"They were nice and bright and were always in the game."
Stoke had a penalty appeal turned down in the last few minutes after Crouch took a tumble in the box, with replays suggesting that the striker may have been caught by his own player, a notion that Hughes vehemently dismissed.
He added: "In the end we're disappointed because we felt there were a couple of penalty decisions that we felt could have gone our way.
"It would have been a little bit unfair on Swansea, who will say that they probably had opportunities to score more goals.
"I've looked at it again, the referee seems to think that it was one of our players that had tripped him, which wasn't the case, so we're a bit aggrieved by that and more so that he booked Crouch afterwards."
But overall, the Welshman was happy to claim a point from a game that he claims his side would previously have lost.
"It was one of those days from our point of view we would have almost certainly lost that game a few weeks ago," he said. "So it's a point where we haven't played particularly well and we have to be grateful for that."
The result leaves Stoke still in the relegation mix, with Hughes' men now three points away from danger ahead of their trip to his former employers Manchester City at the weekend.
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