Actually, the biggest mistake they made was not prosecuting the Confederate Traitors. That got us 100 years of Jim Crow.
Just like not prosecuting the warmongers of the Second Reich brought us the Third Reich.
They tried to. They went through various lawyers trying to take on the case. But after these lawyers studied up on the case, they resigned from it. The case was a loser for the North. Below quotes from (When In The Course Of Human Events, Charles Adams, Rowman & Littlefield Publishers, Inc., 2000)
"A year passed after the withdrawal of John J. Clifford. Another special counsel was appointed to handle the case, the famous author and lawyer Richard Dana of Boston, who had written the great novel 'Two Years before the Mast'. But he too decided the case was a loser. He wrote a lengthy brief, given to the president, taking Clifford's position. Dana argued that a conviction will settle nothing in law or national practice not now settled ...as a rule of law by war.
"Thus as Dana observed, the right to secede from the Union had not been settled by civilized means but by military power and the destruction of much life and property in the South.
The North should accept its uncivilized victory, however dirty its hands might be, and not expose the fruits of its carnage to scrutiny by a peaceful court of law. President Johnson then appointed a new attorney general but he wanted no part of the case and left it to the staff already working on it." p.(186)
President Johnson tried to pardon Jeff Davis to avoid the trial. Davis refused the pardon. He wanted a trial. He wanted his day in court.
To make Davis a traitor, as the North claimed, secession must be proved to be illegal and unconstitutional. They knew they couldn't do it. The idea of their military victory not being supported by law, was too much for them to take a chance on.
Thus, through another dog and pony show, by Chase, head of the Supreme Court, they just opened the cell door and told Jeff Davis to go away. The most hated man in the North was set free.
The only other thing they could do, as they did with many before, was just by military mob rule, drag him out of prison and just hang him. But, Lincoln was dead, courts, which he trampled on, were back in session. The rule of Law was back. The Constitution was back.
The North was the traitor.
Quantrill