In Compton scattering with neutrons in the energy range 20-120 eV, it has been observed that the relative H/M cross sections in a variety of H-containing materials are 20-40% lower than expected from the composition ratio H/M (M being a heavier element in the same compound). The same phenomenon has also been observed in Compton scattering with electrons of 2 and 20 keV energy. There is, at present, no consensus about the reason for these anomalies. In this theory, they are explained as a result of interference when the scattering particle interacts with more than one hydrogen nucleus. The coherence volume of the actual setup, which limits the number of interfering particles, is therefore an important parameter. It is shown here that the large zero-point motion of the hydrogen nuclei leads to reductions in the scattering intensity from interfering pairs. Coherence is preserved over the sub-fs scattering times relevant for this process, even in the condensed systems studied. It is gradually lost when the scattering time is increased, which happens when the neutron energy is reduced (as reflected in lower anomalies for smaller scattering angles). Explicit expressions for the decoherence effect are presented and compared with experimental observation for a selection of observed H-and D-containing systems.