What caused Union garrisons at Harpers Ferry and Martinsburg to seem isolated from the main Union army in 1862?

As it turned out, confusion at the Union's high command actually caused a problem for General Lee. Both garrisons at Harper's Ferry and Martinsburg had become isolated from the main Union forces. Part of this was confusion between Union generals McClellan and Halleck as they quarreled over the lines of authority between them.

On top of that was that the two garrisons in question were at the time not attached to any field army. They were under control of the Military Department of Maryland and Southern Pennsylvania. Their commander was General John Wool who had his office in Baltimore.

The mentioned departments were nothing but an administrative entity.

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