Toothpaste Factory - Render Layers Prob.

Hey guys, aint been blendering for a while, havent touched it for about six months so Im a little rusty.
Just doing this little bit of a thing for a short film, trying (for the first time) to break up the scene into render layers and comp it back together.

But the shadow passes and things dont seem right.

for example.

these black wholes appear on the shadow pass but are not there in the combined (comped by blender) image. I cant then comp it to anything without the black holes. Anyone any thoughts?

1st image is blenders combined comp.
2nd is the funky shadow pass
3rd is the shadow pass comped onto the floor as a post process