Tom seems to have become the liaison between Michael and Fredo after Fredo made his fatal slip-up at the Superman show in Havana ("Johnny Ola brought me here..."). When Michael returns to Nevada, he asks Tom where Fredo is, and tells him to get word to Fredo that he knows Fredo was misled, etc. Later, after Michael learns that Pentangeli is alive, he revisits Fredo with Tom:

MICHAEL
What about FREDO? What does he know?
TOM
He says he doesn't know anything -- and I believe him. ROTH well he -- he played this one beautifully.
MICHAEL
I want to talk to FREDO.

If Fredo told Tom that he didn't know anything about Pentangeli, then he was obviously lying because he told Michael at their boathouse meeting that he knew that Pentangeli was alive, and that the Senate lawyer, Questadt, "belongs to Roth."

Why would Fredo lie to Tom, who seemed to be on his side, and tell the truth to Michael? Your thoughts?