The unsteady flow physics due to interactions between a separated shear layer and film cooling jet apart from excitation of periodic passing wake are studied using large eddy simulation (LES). An aerofoil of constant thickness with rounded leading edge induced flow separation, while film cooling jets were injected normal to the crossflow a short distance downstream of the blend point. Wake data extracted from precursor LES of flow past a cylinder are used to replicate a moving bar that generates wakes in front of a cascade (in this case, an infinite row of the model aerofoils). This setup is a simplified representation of rotor-stator interaction in a film cooled gas turbine. The results of numerical simulation are presented to elucidate the formation, convection and breakdown of flow structures associated with the highly anisotropic flow involved in film cooling perturbed by convective wakes. The various vortical structures namely, horseshoe vortex, roller vortex, upright wake vortex, counter rotating vortex pair (CRVP), and downward spiral separation node (DSSN) vortex associated with film cooling are resolved. The effects of wake on the evolution of these structures are then discussed.