While it was speculated that 5$d^4$ systems would possess non-magnetic $J$~=~0 ground state due to strong Spin-Orbit Coupling (SOC), all such systems have invariably shown presence of magnetic moments so far. A puzzling case is that of Ba$_2$YIrO$_6$, which in spite of having a perfectly cubic structure with largely separated Ir$^{5+}$ ($d^4$) ions, has consistently shown presence of weak magnetic moments. Moreover, we clearly show from Muon Spin Relaxation ($mu$SR) measurements that a change in the magnetic environment of the implanted muons in Ba$_2$YIrO$_6$ occurs as temperature is lowered below 10~K. This observation becomes counterintuitive, as the estimated value of SOC obtained by fitting the RIXS spectrum of Ba$_2$YIrO$_6$ with an atomic $j-j$ model is found to be as high as 0.39~eV, meaning that the system within this model is neither expected to possess moments nor exhibit temperature dependent magnetic response. Therefore we argue that the atomic $j-j$ coupling description is not sufficient to explain the ground state of such systems, where despite having strong SOC, presence of hopping triggers delocalisation of holes, resulting in spontaneous generation of magnetic moments. Our theoretical calculations further indicate that these moments favour formation of spin-orbital singlets in the case of Ba$_2$YIrO$_6$, which is manifested in $mu$SR experiments measured down to 60~mK.
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