From what we saw in the movie -

Tom "He's a good lawyer” but was not up to the job of wartime Consigliere [perhaps not even peacetime Consigliere!]

Besides the two instances you have referred to - Pentangeli's survival and Fredo knowing plenty including Senate lawyer, Questadt, belonged to Roth - happened towards the end of Godfather II and did not really result in the Corleones' misfortunes as such
Certainly caused grief but Michael ended up beating the perjury rap

Whilst Tom may have been incompetent as Consigliere I still don't see any evidence? that supports this theory “Michael blamed and continues to blame Tom for the Corleone's misfortunes”