It was claimed that captain Ryan Shawcross told off striker Kenwyne Jones for publicly criticising the former boss and an argument involving several players ensued.
Hughes said: "That was a fabrication. It never actually happened.
"I don't know why the guy who wrote the story seemed to want to go down that route.
"Whether or not he has got an agenda and is trying to be mischievous, I have no idea. It certainly didn't happen."
Stoke owner Peter Coates has since asked players to stop speaking publicly about Pulis.
Hughes said: "Mr Coates has mentioned that it is unhelpful to keep bringing Tony up and I fully agree with that.
"But there was never any bust-up. It was a total fabrication."
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