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I recently rewatched the Man Behind the Curtian and put something together.
In 1973 when Ben runs into the jungle, he hears the whispers all around him for a few minutes and then Richard walks out of the jungle. This being Ben's first encounter with the Hostiles he knows nothing about them so it is fairly natural for a child to conclude the whispers were caused by or controlled by Richard and the Hostiles at the time. Even after being healed in 1977, we know that Ben continued to live with DHARMA until the purge in 1992, so he would not be well versed in what the Others know.
In 1989 when Ben kidnapped Alex and said the famous line about the whispers, he was still living full time with DHARMA. I belive he was still operating under his incorrect assumption that the whispers were a device of the Others at the time.
I see Ben during this time as very much like Locke in 2004, he deeply belived in the island, but didn't really understand what he was talking about and so had a few things wrong.
It is worth noting that Ben never again associates the whispers with the Others after becoming the leader and presumably finding out that the Others did not control this phenomenon.