Jones was missing from the Potters' matchday squad when they were beaten 5-3 at the Britannia Stadium in the league on Sunday.
It was subsequently reported that the 29-year-old Trinidad and Tobago international - rumoured to be a transfer target of Everton - had sent a text message to Hughes on the night before the contest to say he was unavailable for selection and, as a result, had been fined the equivalent of two weeks' wages.
Asked about that on Thursday at his press conference to preview the Palace clash, 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.
"But moving forward, we'll have to wait and see."
When asked about the talk of Everton being interested in Jones, 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."
He added: "Sometimes you make mistakes and on this occasion Kenwyne made a mistake. I accept that sometimes that can happen."