The controversial second-half incident was one of few moments of interest in largely dull Barclays Premier League contest.
The Baggies' Stephane Sessegnon was twice denied by the excellent Asmir Begovic, including in the last minute after a mazy run through the Stoke defence when he probably should have scored.
Hughes said: "We are grateful to Asmir at the end. That is an outstanding save.
"Given the time of the chance, if they had scored then they would probably have taken the game away from us.
"They will feel a bit aggrieved with the penalty claim they had - it looked like it was a penalty.
"But we had similar complaints a couple of weeks back at Fulham. As the old adage goes, they even themselves out. Apparently."
Stoke have scored just four times in the league this season and Hughes is growing concerned, even though he remains happy with the number of chances they are creating.
He said: "We are struggling for goals but that was prevalent before I came here.
"It is something we are working on. In terms of chances we are still creating the same, if not more, given we are playing in a slightly different way.
"It is up to us to make sure we convert the ones we get.
"We had a number of chances here, a number of balls flashing across the six-yard box, just needing a touch to convert them, and Stephen Ireland had a great opportunity.
"They had a number of chances in the first half when we were a little bit passive in our work but, apart from the one at the death, they didn't create that many more."