The Potters were awarded an injury-time penalty at the Liberty Stadium, which was converted by Charlie Adam, to force a 3-3 draw with the Swans which came after the visitors led by two goals at the break.
Swansea dominated proceedings in the second half to take a 3-2 lead before the questionable penalty came for an apparent handball against Wayne Routledge in the area.
Hughes said Stoke gained some luck with the decision but said that is part and parcel of football sometimes.
"I have seen it and I can understand why Swansea are aggrieved about it, but those things can go for you or go against you and we are grateful we got a break,” he said.
"It still had to be dispatched and Charlie did well as he had not been on long and showed good mental strength to get us a point, which at that stage it looked like we were not going to get.
"In the first half we were excellent, we came with a gameplan and executed it.
"We knew there would be a response, we knew they would put us under pressure, and we could have handled it better.
"To concede three goals in the manner we did was not what we have been about this season."
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