I'm talking about Ex Parte Milligan [See link below]. The majority ruled that it was unconstitutional to subject a citizen to trial by military tribunal in a state that was not in rebellion where the courts were open. The minority opinion, written by Chase, agreed with that the tribunal did not have jurisdiction over Milligan because the Act of Congress did not authorize it, but dissented as to whether Congress had it within its power to do so. Neither the majority nor dissent take Lincoln directly to task, but they do rule against the tribunals that were set up on his watch - which you wouldn't think they would do if they were simply trying to vindicate every northern war measure.

The whole case is 106 pages long, but the opinion and dissent are in the last 26 - it was common in earlier Supreme Court cases to report the arguments of counsel before the actual opinion, which makes for some extremely long cases.

The interesting thing is that this opinion was discussed during WWII vintage cases and again most recently in dealing with the Guantanemo Bay detainees.