The reason Frankie is complainting about Michael not taking the Fifth is that it meant Frankie would have to go before the committee and testify that he got direct orders from Michael to murder people and to commit other crimes. The only evidence the committee had was from Cicci, who said he never received a direct order from Michael Corleone to do anything illegal. This meant that their case against Michael was circumstantial at best.

Pentangeli made an immunity deal in which he was not prosecuted for anything, and got to live under Federal protection outside of a prison in exchange for an affidavit implicating Michael in criminal activity, and he also promised to testify against Michael if necessary. This means he broke Omerta, and disgrace himself annd his family.

He was hoping Michael would take the fifth, which most people see as admitting guilt. When he didnt, Frankie knew he would be the next person called.