Reports have suggested Bony, on loan from Manchester City, is at the centre of unrest, with Hughes and his players questioning the striker's attitude and work rate.
But Hughes, speaking ahead of Saturday's Premier League home clash with West Brom, said: "Wilfried has come in and had a real positive impact on the group.
"We have been delighted with his character and what he has shown.
"In terms of what he's been able to produce on the pitch, he hasn't played too many games in the last couple of years, he is three games into his Stoke career and he is getting up to speed.
"To say we are questioning his attitude or what he is bringing to the party is totally wrong."