This is dependent on your original mesh, that you have converted to xdmf format. You should inspect the facet_mesh file in for instance paraview, to see if you spot anything. I would also suggest to look at the generated mesh, mesh.xdmf with paraview to make sure it looks Like what you expect.
See for instance: Transitioning from mesh.xml to mesh.xdmf, from dolfin-convert to meshio - #62 by dokken