Tom found out about Pentangeli's survival from the Senate committee (either the chair or Questadt) because they were required to disclose to him the witness they were about to use against his client (Michael). Fredo probably did tell Tom he knew nothing--then, when he was with Michael, he blurted out that he knew Pentangeli was alive, and that Questadt belonged to Roth. That would have made Tom look like a fool for telling Michael, just a bit earlier, that "He says he doesn't know anything--and I believe him." Not the stuff to ensure warm feelings all around.