It was reported that Jones - understood to be a transfer target of Everton - had sent a text message to Hughes on the eve of Sunday's Sky Live clash with Liverpool to say he was unavailable for selection.
When questioned further on the matter, Hughes said: "What was reported was what happened.
"I was disappointed and Kenwyne has been fined because it is not something that should happen.
"We spoke on Monday just to get an understanding of why it happened, so we had that meeting.
"He has been in this week training and we get on with it. He won't be involved this weekend, that would be fair to say, because maybe the events of last weekend are still in his mind."
When asked about the talk of Everton being interested in Jones, who has six months left on his current contract, Hughes said: "Maybe that's the problem - that maybe people are telling him there are clubs in for him.
"We've had no contact from anybody in this window, so maybe the information isn't what it seems from the outside.
"But we'll have to wait and see. The transfer window is open and a lot of things happen in a window.
"We'll have to bide our time. But it is unfortunate - none of us saw it coming, so we are disappointed.
"Sometimes you make mistakes and on this occasion Kenwyne made a mistake. I accept that sometimes that can happen."