The code for problem described in (http://cgal-discuss.949826.n4.nabble.com/Mesh-deformation-produces-strange-results-td4662924.html)

MeshDeformation.cpp

typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
typedef K::Point_3 Point_3;
typedef CGAL::Surface_mesh<Point_3>                  Mesh;

typedef boost::graph_traits<Mesh>::vertex_descriptor    vertex_descriptor;
typedef boost::graph_traits<Mesh>::vertex_iterator        vertex_iterator;
typedef boost::graph_traits<Mesh>::halfedge_iterator    halfedge_iterator;

typedef CGAL::Surface_mesh_deformation<Mesh, CGAL::Default, CGAL::Default, CGAL::Deformation_algorithm_tag::SRE_ARAP> Surface_mesh_deformation;
    
void deformMesh(Mesh &cgalMesh, int* ctrlPtIdx, Vector3* targetPositions, int pointCount, int iterations, double tolerance)
{
	// Create a deformation object
	Surface_mesh_deformation deform_mesh(cgalMesh);

	deform_mesh.set_sre_arap_alpha(0);

	// Definition of the region of interest (use the whole mesh)
	vertex_iterator vb, ve;
	boost::tie(vb, ve) = vertices(cgalMesh);
	deform_mesh.insert_roi_vertices(vb, ve);

	vector<vertex_descriptor> _ctrlPtIdx;
	vector<Surface_mesh_deformation::Point> _targetPositions;

	for (int i = 0; i < pointCount; i++) {
		vertex_descriptor control_p = *CGAL::cpp11::next(vb, ctrlPtIdx[i]);
		_ctrlPtIdx.push_back(control_p);
		deform_mesh.insert_control_vertex(control_p);
		_targetPositions.push_back(Surface_mesh_deformation::Point(targetPositions[i].x, targetPositions[i].y, targetPositions[i].z));
	}

	cout << "Preprocessing..." << endl;
	bool is_matrix_factorization_OK = deform_mesh.preprocess();

	if (!is_matrix_factorization_OK) {
		std::cerr << "Error in preprocessing, check documentation of preprocess()" << std::endl;
		return;
	}		

	for (int j = 0; j < pointCount; j++)
		deform_mesh.set_target_position(_ctrlPtIdx[j], _targetPositions[j]);

	cout << "Deforming..." << endl;
	deform_mesh.deform(iterations, tolerance);

	cout << "Saving..." << endl;

	// Save the deformed mesh into a file
	std::ofstream out1("deform.off");
	out1 << cgalMesh;
	out1.close();
}