The present paper describes the application of proper orthogonal decomposition (POD) to large eddy simulation (LES) of the T106A low-pressure-turbine profile with unsteady incoming wakes at two different flow conditions. Conventional data analysis applied to time averaged or phase-locked averaged flow fields is not always able to identify and quantify the different sources of losses in the unsteady flow field as they are able to isolate only the deterministic contribution. A newly developed procedure allows such identification of the unsteady loss contribution due to the migration of the incoming wakes, as well as to construct reduced order models that are able to highlight unsteady losses due to larger and/or smaller flow structures carried by the wakes in the different parts of the blade boundary layers. This enables a designer to identify the dominant modes (i.e., phenomena) responsible for loss, the associated generation mechanism, their dynamics, and spatial location. The procedure applied to the two cases shows that losses in the fore part of the blade suction side are basically unaffected by the flow unsteadiness, irrespective of the reduced frequency and the flow coefficient. On the other hand, in the rear part of the suction side, the unsteadiness contributes to losses prevalently due to the finer scale (higher order POD modes) embedded into the bulk of the incoming wake. The main difference between the two cases has been identified by the losses produced in the core flow region, where both the largest scale structures and the finer ones produces turbulence during migration. The decomposition into POD modes allows the quantification of this latter extra losses generated in the core flow region, providing further inputs to the designers for future optimization strategies.