Ex Parte Milligan and Mary Surratt

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So let me see if I have this right. At the time of MES trial and execution the Supreme Court had before it the case of Mr Milligan ? Yet they did not issue a stay for MES and the others while they were deciding Mr Milligans case. Wouldn't this be standard operating procedure today? Why not then? Can anyone give me an idea of some of the dynamics in the case of the conspirators that allowed their case to go on. Was it stricktly that Washington DC and Milligans state of Indiana were viewed differently as to their status in the rebellion or was it that the court didn't operate that way in 1865? Help !!