Photo: https://dl.dropboxusercontent.com/u/59263671/Why%20can%27t%20i%20command%20this%20fleet.png
For some reason, for that little fleet of 2 ships, I could not bring up the Command Screen. On a related note, I don't think all the buttons on that screen work properly. I tried telling a transport that I had stacked with the fleet to "guard", so it would stop coming up as idle, and it didn't seem to want to work.