I'm rendering a scene that I created with some assets and trees from Sapling Tree Gen. But in my rendering there are these weird pixels/shadows and when I look closely I notice that some bushes don't seem to use their alpha channel. I only use 3 types of bushes in the rendering.
I believe this happens because cycles sets a limit on how many times transparency can overlap before it stops calculating; by default it's set to 8. Anything above 8 layers of transparency will just render as black. This can be increased in the render tab under Light Paths > Max Bounces > "Transparent"
I setup a little scene here that visualizes it. It's just a plane with an array modifier and a principled shader with its alpha set to 0.2