While re-mapping an area of  a world I use for testing I spotted many random shadow areas. Some just in the sky, others, as shown in the images, go from the ground to the max height you can fly.

If this was just in the old chunks areas I might understand but these are happening in the revised/new chunk areas.

Placing a torch will remove the darkened area as it would in a cave or mine and as you might expect, once you remove the torch the darkness returns.