Reports claimed the South African got changed and went home in anger after being taken off in the 61st minute of Rovers' 3-1 Barclays Premier League win at Ewood Park.
Hughes claims no such thing happened and insists there has been no need for "clear-the-air" talks with his top scorer.
Hughes said: "People keep on telling me that he has stormed off down the tunnel and 'left the building', so to speak, but I spoke to Benni about it after the game.
"Obviously, he was dressed in his suit because he had been taken off early but he was still there at the end of the game.
"It's just one of those stories where possibly people are trying to make mischief, that's all it was. We're fine."