If they weren't all idiots, someone at the Black Site should tell Liz that Reddington was in Nebraska when her father died. And, for that matter, both Black Site and whoever is watching the Keanes should have followed Tom out of town, as it's easy to meet someone while traveling or otherwise engage in hanky-panky.
I'm not sure whether Liz should expect Tom to recognize Reddington, as opposed to just knowing the name. Tom saw the board with pictures of Reddington's flunky and I think Reddington's picture was there as well. Should she be suspicious that Tom didn't report the conversation? And, is Tom pretending not to recognize Reddington absolutely conclusive proof that Tom is a villain? And since he went to the trouble of framing Reddington, why wouldn't he want to cause Reddington even more trouble by suggesting that Reddington killed Sam? (That it would be a true charge is irrelevant.