We present a detailed analysis of the dynamics of photon transport in waveguiding systems in the presence of a two-level system. In these systems, quantum interference effects generate a strong effective optical nonlinearity on the few-photon level. We clarify the relevant physical mechanisms through an appropriate quantum many-body approach. Based on this, we demonstrate that a single-particle photon-atom bound state with an energy outside the band can be excited via multiparticle scattering processes. We further show that these trapping effects are robust and, therefore, will be useful for the control of photon entanglement in solid-state based quantum-optical systems.