What I don't get about "there's a lot I can't tell you" is that he is obviously referring to the Roth deal in Cuba because earlier that day he asked Tom to leave the room before he and Johnny Ola talked. Yet when Michael and Fredo escaped Cuba, Tom seemed to know everything about it, right down to what happened to Roth. When did he learn of all this?
Michael more than likely filled Tom in on the Cuba details later, of course choosing only to inform Tom of the details Michael deemed necessary. Enough for Tom to know where Michael would be, but not the intimate details of the Cuba trip.