Of course, alot of the gaps in interaction between the characters is a function of what FFC wanted to portray on the screen and what was left on the cutting room floor.

Michael explodes at Tom for not directly answering his questions because FFC wanted us to see a new Michael experiencing the stress of betrayal and uncertainty in a world where murder is just a shot away. He wants it all to contrast with Vito's world where Vito was surrounded with people of unquestioned loyalty. I think he also wants to portray Tom as the one thing that remains constant regardless of Michael's attitude toward him.

Maybe there was a phone call between Fredo and Tom that was filmed, but didn't make it into the final cut. But I don't see Fredo telling Tom about his betrayal. It's possible that even at that point Fredo didn't see it as a betrayal. Also, even though Michael knew why Fredo might be scared, Tom didn't. So, why would Michael tell Tom that "I know he's scared"? At that point, if Tom hadn't talked to Fredo, Tom had to be wondering why Fredo was scared and about what Roth had mislead him.