GaN boules were grown up to thicknesses of 6.3 mm via vertical HVPE on 2 in. GaN/sapphire templates. The usable boule length is limited by surface defects. Two different sub-surface disturbances were identified to be responsible for these surface defects using optical inspection and low-temperature photoluminescence on polished m-plane slices cut from the boules. One disturbance starts already at the interface to the used template resulting in large V-pits at the surface. The other one occurs after undisturbed GaN growth of several mm and leads to local cracking networks and small V-pits at the surface. Both lead to deteriorated structural properties of subsequently grown material with red-shifted and broadened exciton emission. In contrast, the undisturbed material having a smooth surface is of high material quality and shows constant energies of the exciton emissions with narrow line widths.