The complex interaction of an atomic projectile with a molecular target is studied by considering the time-dependent electron-nuclear dynamics of the collision. We calculate the energy loss, charge exchange, and differential cross section for a hydrogen beam colliding with molecular hydrogen targets for projectiles energies from 10 eV/amu up to 25 keV/amu. We obtain the total, electronic, nuclear, and rovibrational contribution for the orientationally averaged stopping cross section of the molecular target when scattering over all the angles is considered. We emphasize the violation of Bragg's rule (additivity of the atomic energy loss for the compound target) and the acceptance angle dependence of the experimental stopping cross section.