We investigate charge transport across metal-molecule-metal junctions, i.e. hexagonal and triangular nanographene molecular layers sandwiched between Pt and Pd thin films, as measured by ballistic-electron-emission spectroscopy (BEEM). The measured shape of current-voltage curves cannot be explained in the framework of existing BEEM theories of bulk inorganic semiconductors. We develop a tight-binding model for the BEEM process and propose that the energetic dispersion of molecular layers and the dephasing effect due to the interface states account for the anomalous BEEM current-voltage behavior and play an important role in determining the shape of the curve. The electron-phonon scattering can also affect the shape of current-voltage curves.