Is there indexed geometry? Let those two verts on diagonal be shared in both triangles.
They should be not just identical, but the very same instances.

"In this recipe, we'll use SSBOs and image load/store to implement order-independent transparency. We'll use two passes. In the first pass, we'll render the scene geometry and store a linked list of fragments for each pixel. After the first pass, each pixel will have a corresponding linked list containing all fragments that were written to that pixel including their depth and color. In the second pass, we'll draw a full-screen quad to invoke the fragment shader for each pixel. In the fragment shader, we'll extract the linked list for the pixel, sort the fragments by depth (largest to smallest), and blend the colors in that order. The final color will then be sent to the output device." some thing like that

It sounds like what vstrakh is suggesting. Do you have 4 vertices per quad or 6? From how you say the algorithm works it sounds like along that line it has 2-3 values per pixel. 3 where the red and green over lap and 2 where the green is. To check you could modify the shader to set different colors depending on the size of the linked list. It seems like you have 6 vertices and the corner vertices are ever so slightly different so it is making the two triangles that make up the green quad overlap (thus giving you 2-3 values per pixel along the overlap).