The transport properties of epitaxial graphene on SiC(0001) at quantizing magnetic fields are investigated. Devices patterned perpendicularly to SiC terraces clearly exhibit bilayer inclusions distributed along the substrate step edges. We show that the transport properties in the quantum Hall regime are heavily affected by the presence of bilayer inclusions, and observe a significant departure from the conventional quantum Hall characteristics. In particular, we observe anomalous values of the quantized resistance and a peculiar asymmetry with magnetic field which was not observed before for graphene on SiC. A quantitative model involving enhanced inter-channel scattering mediated by the presence of bilayer inclusions is presented that successfully explains the observed symmetry properties.