Stoke picked up all the points with a 2-1 win, but the victory has been marred by a penalty incident in the first period, when Victor Moses went to ground very easily under pressure from Swans defender Angel Rangel.
Charlie Adam stepped up to convert the spot kick, which levelled the scores in the latter stages of the first period.
Monk claimed that his side were "cheated", but Hughes has branded those comments "unacceptable" and believes that Monk's inexperience could land him in trouble.
"With Victor Moses' pace in the box, Angel Rangel has come across him and impeded him in my view. It doesn't take too much at that pace. I actually heard him [Swansea manager Garry Monk] say my player is a cheat, which is unacceptable in my view," he told Sky Sports News.
"Obviously he is upset, and we have to come in here and speak 20 minutes after the game but sometimes you just have to bite your tongue, maybe that will come with experience."