Going into Part II (and repeating what I posted earlier): Fairly or not, Michael may have blamed Tom at least partly for Sonny's death and held it against him because if Sonny had lived, Michael wouldn't have had to assume the Donship. And again, Tom was Vito's choice as consigliere, not Michael's; and Sonny, not Michael, brought him home to be his brother.
In Part II, Tom screwed up big time by not finding out that Pentangeli had survived the Rosato brothers' rubout attempt. Thinking Frankie dead, Tom advised Michael to lie under oath. Tom told Michael, "Our people with the NY detectives said he [Frankie] was half dead, talking out loud about how you betrayed him..." DUH, Tom: where were your people with the NY detectives before you advised your client to commit five counts of perjury, which very nearly landed him five consecutive five-year prison sentences? Michael also may have blamed Tom for Kay's abortion. Yes, I know that she arranged it, but it happened on Tom's watch, when Michael had charged him with keeping her and the kids under lock and key.
No one was more loyal to Michael than Tom. I believe Michael treated Tom badly. But Tom was less than a great consigliere.