The instability and dynamics of a vertical oscillatory boundary layer in a container filled with a stratified fluid are addressed. Past experiments have shown that when the boundary oscillation frequency is of the same order as the buoyancy frequency, the system is unstable to a herringbone pattern of oblique waves. Prior studies assuming the basic state to be a unidirectional oscillatory shear flow were unable to account for the oblique waves. By accounting for confinement effects present in the experiments, and the ensuing three-dimensional structure of the basic state, we are able to numerically reproduce the experimental observations, opening the door to fully analysing the impacts of stratification on such boundary layers.