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The Supreme Court heard Ex Parte Milligan after the war. SCOTUS almost heard another case concerning military commissions but one was all the lunatic wacko fringe radical Congress would allow.

The Court announced in 1868 it was going to hear arguments in Ex Parte McCardle in another challenge to military commissions. McCardle had been convicted by a military commission for publishing inflammatory articles condemning reconstruction in the south. He had been denied a writ of habeas corpus under the habeas corpus act of 1867.

The Congress moved to prevent the case from being heard. Over President Andrew Johnson's veto, Congress enacted a statue known as the McCardle repealer, denying the Supreme Court appellate jurisdiction in habeas corpus petitions brought under the habeas corpus act of 1867.

Article III, section 2, renders SCOTUS appellate jurisdiction subject to "such exceptions . . . as the Congress shall make." In 1869 SCOTUS accepted that its appellate authority had been voided in the case. McCardle found his access to the Supreme Court had been eliminated.

Access to the Supreme Court extended only so far as the Court refusing to hear a case, or not granting relief when a case was heard.

In 1863, it appears that SCOTUS reported all of four cases.

Pomeroy's Lessee v. State Bank of Ind., 1 Wall. 23 (1863)
Hardy v. Johnson, 1 Wall. 371 (1863)
Roosevelt v. Meyer, 1 Wall. 512 (1863)
Houghton v. Jones, 1 Wall. 702 (1863)

The Vallandigham case occurred during the war, but SCOTUS did not consider the merits, claiming lack of jurisdiction.

2 Black. - 1862 Term

CASE CITATION FINDER
1790-1862 Terms (1 Dall.-2 Black)

1 Wall. -- 1863 Term

CASE CITATION FINDER
1863-1889 Terms (1 Wall.-136 U. S.)

Clarification:

It has come to my attention that a number of cases from the 1862 term, listed under 2 Black., have report dates in the first quarter of 1863.

For the 1863 term, 1 Wall. lists only four cases being reported in 1863.

The above links go to the official SCOTUS site and provide case citations by term.