Hughes was expecting to be without his 30 year old leading goalscorer for up to a month in the New Year whilst he participated in the tournament, which is taking place in Ghana in January.
There was a suggestion, denied by Hughes, that a deal had been struck with the South African FA.
"It was a surprise to Benni initially that he got called back into the squad earlier this year," Hughes told the Lancashire Telegraph.
"But it was a new manager and, obviously, he wanted to see what options he had.
"Maybe that's behind it.
"I'd have to speak to Benni because I was unaware of it.
"We haven't put any pressure on Benni or South Africa not to include him, and we were preparing to be without him."