Zig-zag surface after skinning

I have a cylindrical model, which consists of an outer and an inner layer, each having their own mesh and vertices. I have skinned this cylinder to multiple spheres so that when the spheres move around, they deform the mesh of the cylinder. However, at runtime when the spheres lay flat on the ground, the skinned model has a rough inconsistent surface on the bottom. Any ideas as to how to get rid of the rough surface? Is this because the cylinder model has a low vertex count?