We show that in non-collinear magnetic molecules, non-adiabatic (dynamical) effects due to the electron-vibron coupling are time-reversal symmetry breaking interactions for the vibrational field. As in these systems the electronic wavefunction can not be chosen as real, a nonzero geometric vector potential (Berry connection) arises. As a result, an intrinsic nonzero vibrational angular momentum occurs even for non-degenerate modes and in the absence of external probes. The vibronic modes can then be seen as elementary quantum particles carrying a sizeable angular momentum. As a proof of concept, we demonstrate the magnitude of this topological effect by performing non-adiabatic first principles calculations on platinum clusters and by showing that these molecules host sizeable intrinsic phonon angular momenta comparable to the orbital electronic ones in itinerant ferromagnets.