The Trinidad & Tobago striker made himself unavailable to take on the Reds on Sunday, sending Hughes a text to inform of his decision not to play.
But the disobedient move has cost Jones a fiscal sanction with Hughes also confirming he will miss this weekend's meeting with Crystal Palace.
"What was reported was what happened," Hughes told reporters.
"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."
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