We have combined atomic force microscopy (AFM) and 2D + 1 Monte-Carlo simulations to investigate the formation of local potential minima in self-ordered AlGaAs/GaAs V-groove quantum wires. In order to determine the origin of these potential fluctuations along the wire axis in the sub-micrometer range, we studied by AFM the morphology of V-grooved substrates at different stages of processing and growth. Monte-Carlo simulations are used to study the influence of the growth kinetics on the self-limiting profile in disordered V grooves. Our model evidences a re-entrant mechanism in which the sidewalls roughness induces monolayers thickness fluctuations along the wire axis. The influence of the growth conditions on the quantum wire disorder is discussed.