Butland escaped punishment for his 17th-minute challenge outside the area on Andre Ayew, the Stoke goalkeeper going in studs first on the Ghanaian after his bad touch had allowed the ball to run loose.
Ayew had to take evasive action and referee Robert Madley waved play on, but Hughes was unhappy that the incident was replayed three times on the big screen from different angles.
"He (Butland) had to retrieve a situation and I thought he got the ball," Hughes said.
"There was a big shout from the home crowd as you would expect.
"It could have gone against us, in fairness, but if that's a little bit of luck that has gone our way then we'll take it.
"But I didn't appreciate the incident being shown on the videos around the stadium
I thought that was unnecessary.
"I wouldn't like to think it was deliberate, because when those situations happen it causes a reaction in the crowd and we had to deal with that."
Stoke's third successive Barclays Premier League victory was secured by Bojan Krkic's early penalty after the Spanish striker had been felled by Ashley Williams.
It was Bojan's second goal of the season following a serious knee injury which ruled him out for seven months and Hughes could not hide his delight.
"I am pleased with Bojan's performance," Hughes said.
"He made the difference this evening and that was the key moment.
"It was a good away performance, we had a good plan and we executed it really well.
"We were always a threat on the break and did not allow Swansea to get any momentum
In fact I cannot remember Jack having too much to do."
Jonjo Shelvey did strike a post in the second half, but Swansea laboured for large parts of the game and their search for an equaliser was often unconvincing.
The Swans have now gone six games without a win in all competitions and their first home defeat of the season dropped them to 14th place in the Premier League.
"We're in a difficult moment because we're not quite at the levels we need to be," manager Garry Monk said.
"That's disappointing because we all know how capable this group of players are and the football we can produce.
"But it's for me to work with the players, we need to work hard together and stick together and get back to the levels which we know this team can produce.
"We've been in difficult moments but we have to work through it.
"I'd be lying if I said I was not concerned, but I'm not overly concerned.
"We went five games last season without winning and everyone said that was a difficult period and we ended up having a fantastic season."
Source : PA
Source: PA