As far as contacting his spy it is still very possible. For example the spy would be able to use the phones as he/she is masquerading as one of the Freighties and would have access to one. He would also be able to steal a phone without it going totally unnoticed and get it to Ben somehow.
Plus we don't know how long the spy has been on the ship. The two may have been communicating through the Looking Glass for some time. Hence why Brendon (as I agree with Roco) may have destroyed the comms, to prevent the rest of the Freighties from ever finding out they contacted the Looking Glass and the Island. Brendon could very well have been working with the spy, especially if as Roco suggests he is linked with Danielle; and Danielle is interacting with Ben.
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The Enigma Heroes Is Better Than Lost
...heroes never die
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