When in doubt, defer to the Constitution, not to the politically-induced cacaphony out there which passes for wisdom and erudition.
In short, Steven Calabresi, LIBERAL constitutional law professor at Northwestern University, asserts that per Art II's "appointments clause" a special counsel must be appointed by the President and confirmed by the Senate, failing which all of Mueller's actions are null and void, inclusive of all indictments, searches and plea agreements. (Where was Calabresi and others of his ilk when Congress fashioned the ill-begotten special counsel regulations?) In this regard, Calabresi recommends that Flynn and Manafort, among other victims of this witch hunt, challenge the constitutionality of any charges lodged against them by Mueller. (Of course, these victims would need to rely upon judges who may not be as faithful to the Constitution. But the effort is worth taking, I'd say, particularly since the Supreme Court is decidedly more conservative these days.)
Calabresi also points out that Rosenstein's appointment of Mueller ignored 28 CFR 600-1 - 600-10 which stipulates that, among other requirements, a special counsel may be appointed if "a criminal investigation..is warranted". However, Mueller's appointment referred NOT to a criminal matter, but to a counter-intelligence investigation.
And so it goes. When even liberal constitutional experts seriously question the legitimacy of Mueller's appointment, we must all take notice.