The longitudinal distribution of a free-electron laser (FEL) may present a complex internal structure. This phenomenon has been already observed in the case of LINAC based oscillators and self-amplified spontaneous emission devices (for which the presence of "spikes" in the temporal distribution is systematically observed). We investigate here the physical process responsible for the growth of complex substructures inside the micropulse of a storage-ring free-electron laser. This "hole-burning-like" process results from the localized character of the interaction between the ultrarelativistic electron beam circulating in the storage ring and the laser pulse. Experimental results concerning the case of the super-ACO FEL are presented and interpreted by means of a pass-to-pass tracking code containing all the relevant features of the system dynamics.