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Functional thin film superlattices with stability in extreme environments can lead to transformative performance in optical and thermal applications such as thermophotovoltaics. In this work, key issues associated with defects that prevent layer-by-layer growth in epitaxial, low-miscibility oxide superlattices are investigated. Layer protrusions, approximately 8 nm wide and 3 nm thick, arise from a strain relaxation mechanism in 8 nm bilayer superlattices of Ba(Zr0.5Hf0.5)O3/MgO and propagate through the subsequent superlattice layers forming an inverted pyramid structure that is spatially phase offset from the matrix. The density and size of these defects scales with the number of interfaces in the sample, indicating that surface roughness during growth is a significant factor in the formation of these defects. In situ high temperature transmission electron microscopy (1000 °C, in vacuo) measurement reveals that phase decomposition of Ba(Zr0.5Hf0.5)O3 and decoherence of the superlattice is nucleated by these defects. This work highlights that achieving optimum growth conditions is imperative to the synthesis of single-crystalline superlattices with sharp interfaces for optimized performance in extreme environments. [ABSTRACT FROM AUTHOR]