Hybrid systems hold promise to provide an advantage in future quantum technology. Operating such systems outside the classical regime is crucially important to fully realize their potential. We investigate a pulsed quantum nondemolition gate between a cloud of atoms and a mechanical oscillator in distant cavities and demonstrate that this gate is capable of producing nonclassical coincidences of excitations in the disparate subsystems interacting by light. The nonclassicality is justified by evaluation of excitations created simultaneously in both modes beyond any joint classical states of such subsystems. To test the result, we use a nonclassicality witness based on available homodyne tomography of the atomic and mechanical states. Using feasible parameters, we show that it is possible to turn the pulsed dynamics of the state-of-the-art systems into nonclassical coincidences, and illustrate it for the cases of the atom-light, optomechanical, and atom-mechanical hybrid interactions. These tests are necessary to open full investigation of quantum correlations in hybrid systems. Published by the American Physical Society 2024