We systematically investigate the magnetic properties and local structure of Ba2YIrO6 to demonstrate that Y and Ir lattice defects in the form of antiphase boundary or clusters of antisite disorder affect the magnetism observed in this $d^4$ compound. We compare the magnetic properties and atomic imaging of (1) a slow cooled crystal, (2) a crystal quenched from 900degree C after growth, and (3) a crystal grown using a faster cooling rate than the slow cooled one. Atomic imaging by scanning transmission electron microscopy (STEM) shows that quenching from 900oC introduces antiphase boundary to the crystals, and a faster cooling rate during crystal growth leads to clusters of Y and Ir antisite disorder. STEM study suggests the antiphase boundary region is Ir-rich with a composition of Ba2YIrO6. The magnetic measurements show that Ba2YIrO6 crystals with clusters of antisite defects have a larger effective moment and a larger saturation moment than the slow-cooled crystals. Quenched crystals with Ir-rich antiphase boundary shows a slightly suppressed saturation moment than the slow cooled crystals, and this seems to suggest that antiphase boundary is detrimental to the moment formation. Our DFT calculations suggest magnetic condensation is unlikely as the energy to be gained from superexchange is small compared to the spin-orbit gap. However, once Y is replaced by Ir in the antisite disordered region, the picture of local non-magnetic singlets breaks down and magnetism can be induced. This is because of (a) enhanced interactions due to increased overlap of orbitals between sites, and, (b) increased number of orbitals mediating the interactions. Our work highlights the importance of lattice defects in understanding the experimentally observed magnetism in Ba2YIrO6 and other J=0 systems.
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