From The Revit Clinic
When a substrate layer is added to a floor's structure, it will cut the slab edge, rather than the edge cutting through and directly attaching to the slab. While some of you may be aware of possible ways to work around this, I wanted to relay a method as I still see the question float around.
The following screenshot shows the default behavior when you add an edge to a slab with a substrate layer:
To have the edge cut through that layer, first Unjoin the geometry:
Then Join it, making sure to select the edge first and then the slab:
I hope this helps!