Trump's attorneys did not say "the special counsel that prosecuted him was not properly appointed by an act of Congress", Justice Thomas brought this up in oral arguments. Trump's attorneys admitted in oral arguments that they had not brought this up during the appeal, so as an argument it was not saved.

Further more, historically there is no basis for the argument. Special prosecutors, which are different from the "independent counsel" that came about after Nixon; the laws around "independent counsel" expired a while ago.

"Special counsel", and all of the other similarly named, have been around since Marbury. By happenstance, some have been X-members of Congress, Cabinet members, etc... but far from all.

There is a reason why none of the other Justices brought this up, it is absurdist.