We show that shooting methods for homoclinic or heteroclinic orbits in dynamical systems may automatically guarantee the topological transversality of the stable and unstable manifolds. The interest of such results is twofold. First, these orbits persist under perturbations which destroy the structure allowing the shooting method and, second, topological transversality is often sufficient when some kind of transversality is required to obtain chaotic dynamics. We shall focus on heteroclinic solutions in the extended Fisher-Kolmogorov equation.