"We haven't put any pressure on Benni or South Africa not to include him, and we were preparing to be without him," he told the Lancashire Telegraph.
Rovers 30-year old striker is South Africa's top scorer and was called back to the squad when new manager Carlos Alberto Perriera took over, but now it would appear the striker does not feature in his plans.
"It was a surprise to Benni initially that he got called back into the squad earlier this year," said Hughes. "But it was a new manager and, obviously, he wanted to see what options he had, maybe that's behind it."