Hi!
This is an excellent question.
I think that Puzo put the word "fact" in on purpose, but neglected polishing up the second part of the sentence - thus it was indeed a fact. Then, it is pointing to the day of reckoning in the future - so it implies revenge. Finally, Tom didn't dare to ask - which means that the revenge would be really terrible.
From this, my first impression was that the answer would have to do with Carlo's participation in setting up Sonny - but I must admit that this petty matter wouldn't bother any Don but Don Vito. Next I thought that there remained the difficulty of "proving" Mike's innocence - again, it's a private Corleones' affair. In my opinion, the question of succession is not a matter of a public discussion either - so it must be something else still.
For now this nice puzzle has been scheduled for batch processing in the long afterhours - and I may be back with another guess any time.
Best regards.
Alexander