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Superconducting proximity effects that are anomalously long-ranged have recently been reported in manganite/cuprate thin-film heterostructures, and attributed to spin-triplet correlations involving odd-frequency pairing. To probe this novel scenario microscopically, we studied multilayer La2/3Ca1/3MnO3/YBa2Cu3O7− δ (LCMO/YBCO) thin films using scanning tunneling spectroscopy (STS), scanning transmission electron microscopy (STEM), x-ray diffraction and electrical transport. The STS measurements at 4.2 K observed no pairing gaps in the tunneling spectra on bilayer films down to 5 nm LCMO thickness. The atomic-scale STEM data revealed double CuO-chain intergrowths in the YBCO layer that form regions with the socalled 247 lattice structure. These nanoscale 247 regions do not show up in x-ray diffraction, but can physically account for the reduction in superconducting critical temperature (Tc) versus YBCO thickness. As further corroboration, we observed similar Tc reduction in LaNiO3/YBCO multilayers, where LaNiO3 is not ferromagnetic. These results suggest that microstructural defects, rather than magnetism, are responsible for the long-ranged attenuation of superconductivity reported in LCMO/YBCO heterostructures.