The strong excitonic emission of hexagonal boron nitride (h-BN) makes this material one of the most promising candidate for light emitting devices in the far ultraviolet (UV). However, single excitons occur only in perfect monocrystals that are extremely hard to synthesize, while regular h-BN samples present a complex emission spectrum with several additional peaks. The microscopic origin of these additional emissions has not yet been understood. In this work we address this problem using an experimental and theoretical approach that combines nanometric resolved cathodoluminescence, high resolution transmission electron microscopy and state of the art theoretical spectroscopy methods. We demonstrate that emission spectra are strongly inhomogeneus within individual few layer flakes and that additional excitons occur at structural deformations, such as faceted plane folds, that lead to local changes of the h-BN layers stacking order.