Clouds moving in opposite directions Today driving to work I saw a small, isolated horse's mane cloud at about 2000 feet. Directly above it was a small strato-cumulous cloud at 4000 feet and and they were moving in opposite directions. The horse's mane was moving north and the strato-cumulous was moving south.

How could this happen? I imagine there must have been two layers of air, each moving in a different direction. In fact there must have been three layers of air, because the strato-cumulous would have been sitting on one layer and moving with the layer above.
This indicates that there was wind shear. Wind can change direction and speed with height. 

Since air is a fluid, it's wind vectors can change with height. On a large scale, this is called the thermal wind balance. In the ocean, it is Ekman balance. On smaller scales, there isn't really a term that I know of that describes the balance, because it is rather turbulent.

As far as "How could this happen": What you saw was the mean flow over the height of one cloud, followed by the mean flow over the depth of another cloud.