The magnetic excitations in the cuprate superconductors might be essential for an understanding of high-temperature superconductivity. In these cuprate superconductors the magnetic excitation spectrum resembles an hour-glass and certain resonant magnetic excitations within are believed to be connected to the pairing mechanism, which is corroborated by the observation of a universal linear scaling of superconducting gap and magnetic resonance energy. So far, charge stripes are widely believed to be involved in the physics of hour-glass spectra. Here we study an isostructural cobaltate that also exhibits an hour-glass magnetic spectrum. Instead of the expected charge stripe order we observe nano phase separation and unravel a microscopically split origin of hour-glass spectra on the nano scale pointing to a connection between the magnetic resonance peak and the spin gap originating in islands of the antiferromagnetic parent insulator. Our findings open new ways to theories of magnetic excitations and superconductivity in cuprate superconductors.