Cloning a mesh does not clone its material - it just reuses the original one by reference. You can copy the material manually though:
const mesh = new Three.Mesh(geometry, material);
const mesh2 = mesh.clone(); // NOTE This is a "shallow clone", it uses the same geometry and material as the previous mesh
mesh2.material = mesh.material.clone();
mesh2.material.color.set(0xdddddd);
(This applies to cloning other things in Three as well - so as an example, if you’d clone a material, it’d reuse textures of the original one unless you clone them manually.)