Vibrationally resolved resonant Auger spectroscopy (RAS) on bound-continuum transitions enables highly sensitive probing of ultrafast dissociation in molecular core-excited states, where a distinct fragment band arises from Auger decay in dissociation fragments. Here, we theoretically investigate fragment band formation driven by ultrashort X-ray pulses. Unlike conventional molecular bands, fragment RAS peaks exhibit an insensitivity to strong X-ray Rabi oscillations. Numerical simulations on water molecules reveal that combining RAS with a fragment's kinetic energy release spectra enables clear observation of Rabi oscillation when the pulse broadening is smaller than the fragment's vibrational frequencies. This work establishes a framework for controlling ultrafast electron-nuclear dynamics in fragmentation by using X-ray pulses.