We report on accumulation of background Si and O impurities measured by secondary ion mass spectrometry (SIMS) at the sub-interfaces in undoped, Zn- and Mg-doped multi-layer GaN structures grown by hydride vapor phase epitaxy (HVPE) on sapphire substrates with growth interruptions. The impurities accumulation is attributed to reaction of ammonia with the rector quartz ware during the growth interruptions. Because of this effect, HVPE-grown GaN layers had excessive Si and O concentration on the surface that may hamper forming of ohmic contacts especially in the case of p-type layers and may complicate homo-epitaxial growth of a device structure.