We perform a theoretical and experimental study of a system of two ultracold atoms with tunable interaction in an elongated trapping potential. We show that the coupling of center-of-mass and relative motion due to an anharmonicity of the trapping potential leads to a coherent coupling of a state of an unbound atom pair and a molecule with a center of mass excitation. By performing the experiment with exactly two particles we exclude three-body losses and can therefore directly observe coherent molecule formation. We find quantitative agreement between our theory of inelastic confinement-induced resonances and the experimental results. This shows that the effects of center-of-mass to relative-motion coupling can have a significant impact on the physics of quantum systems near center-of-mass to relative-motion coupling resonances.