I can see two things at play here:
1) The glass panel is reflective, which is visible in the alpha channel, so the area around the leaves in the alpha channel will not be 100% black
2) The refraction of the glass panel will not appear as black in the beauty, but it will show the sky instead, if you will not set refraction override to pure black
One solution would be to:
-set direct, reflect, and refract overrides to black in scene setup
-disable reflectivity for the glass material
-then use the alpha channel generated from this render