The Ivorian joined the Potters on deadline day of the summer transfer window after falling down the pecking order at City following Pep Guardiola's arrival as manager.
A report in The Mirror has claimed that Hughes and his staff are unhappy with Bony's lack of effort, while his teammates are also said to be questioning the striker's attitude.
It has also been alleged that record signing Giannelli Imbula, who joined the club from Porto in February, is an unpopular figure in the dressing room.
However, Hughes has rejected the reports, admitting that the speculation over his players is "frustrating".
In this morning's press conference, the 52-year-old told reporters: "Let's nip this story in the bud. Unfortunately we are fair game for some areas of work, who feel they can get easy headlines. It is very predictable, and it all comes up at these times and these situations.
"To question players is totally untrue. Wilfried has come in and made a real positive impact behind the scenes. He hasn't had too many games in the past year and he is still getting up to speed. To say we are questioning his attitude is totally wrong. Some of the guys are struggling for a bit of form. Giannelli played in the week and did fine. He is a clear talent, but if his form, like anybody else, isn't where it should be then he will come out of the team.
"It is frustrating to read these stories, because we have a great group and a very strong dressing room. We played well midweek but lost the game. We didn't get the breaks on the night, but there were positives we can take from it, for sure."
Bony, who scored 25 goals during his season-and-a-half stint at Swansea City, has failed to find the back of the net in his first three appearances for Stoke.
The Potters are currently at the bottom of the Premier League table following four defeats and one draw.