The recent experimental advances in manipulating ultra-cold atoms make it feasible to study coherent transport of Bose-Einstein condensates (BEC) through various mesoscopic structures. In this work the quasi-stationary propagation of BEC matter waves through two dimensional cavities is investigated using numerical simulations within the mean-field approach of the Gross-Pitaevskii equation. The focus is on the interplay between interference effects and the interaction term in the non-linear wave equation. One sees that the transport properties show a complicated behaviour with multi-stability, hysteresis and dynamical instabilities for non-vanishing interaction. Furthermore, the prominent weak localization effect, which is a robust interference effect emerging after taking a configuration average, is reduced and partially inverted for non-vanishing interaction.