This happens when Cycles doesn't have enough transparency bounces set, and so once a ray goes through a certain number of transparent layers, it just colours that pixel black instead of continuing to the final surface.

To fix it, go to the Render tab in the properties editor, then go to "Light Paths" > "Max Bounces" > "Transparent" and turn it up to something like 30 (higher values will raise render times). This happens automatically when scattering with Alpha Trees, but not with Scatter5, or a custom scattering setup