The effect of conical intersections (CIs) on electronic relaxation, transitions from excited states to ground states, is well studied, but their influence on hyperfine quenching in a reactant molecule is not known. Here, we report on ultracold collision dynamics of the hydroxyl free-radical OH with Sr atoms leading to quenching of OH hyperfine states. Our quantum-mechanical calculations of this process reveal that quenching is efficient due to anomalous molecular dynamics in the vicinity of the conical intersection at collinear geometry. We observe wide scattering resonance features in both elastic and inelastic rate coefficients at collision energies below k(B) x 10mK. They are identified as either p- or d-wave shape resonances. We also describe the electronic potentials relevant for these non-reactive collisions, their diabatization procedure, as well as the non-adiabatic coupling between the diabatic potentials near the CIs.