Slitherine

It's February 2nd 1941, and although I am able to purchase and deploy soviet infantry units into Russia, I am unable to assign commanders to units.
Do I have to wait for Germany to declare war on Russia, to do this, or is this a glitch?

Yes you can only deploy units that are available to move and while neutral your units are not available for moving. It should sort the commander to the end of the force pool so that him not placeable does not prevent other units being placed.