We show that on suitably pit-patterned Si(001), deposition of just a few atomic layers of Ge can trigger a far larger flow of Si into the pits. This surprising effect results in anomalous smoothing of the substrate preceding island formation in the pits. We show that the effect naturally arises in continuum simulations of growth, and we identify its physical origin in the composition dependence of the surface diffusivity. Our interpretation suggests that anomalous smoothing is likely to also occur in other technologically relevant heteroepitaxial systems. © 2012 American Physical Society.