Physics-based uncertainty quantification is applied to a boundary layer over a flat plate with a statistically stationary separation bubble to assess sources and dynamics of model error (ME) in two-equation Reynolds-Averaged Navier-Stokes turbulence models in separated flows. Two distinct ME modes are found that correspond to the qualitative behavior of ME in a turbulent wall-bounded flow (upstream of the separation bubble) and turbulent free-shear flow (within the separation bubble), with a superposition of these ME modes in intermediate regions. A complex understanding of ME results as it changes throughout the flow, but is ultimately comprised of the elements of canonical flows.