We investigated the driven dynamics of vortices confined to mesoscopic flow channels by means of a dc-rf interference technique. The observed mode-locking steps in the IV curves provide detailed information on how both the number of vortex rows and the lattice structure in each flow channel change with magnetic field. Minima in flow stress occur when an integer number of rows is moving coherently, while maxima appear when the incoherent motion of mixed n and n+/-1 row configurations is predominant. Simulations show that the enhanced pinning at mismatch originates from quasistatic fault zones with misoriented edge dislocations induced by disorder in the channel edges.