Using an ultrahigh-vacuum scanning tunneling microscope we have discovered evidence for a novel mechanism by which Au vacancy islands form during assembly of alkanethiol monolayers on Au(111). Our results suggest a model whereby excess Au atoms are forced out of the surface layer by relaxation of the compressed herringbone reconstruction. This creates adatoms on, and vacancies in, the surface layer. On large terraces the vacancies nucleate into islands while the adatoms migrate and adsorb at ascending step edges. At saturation coverage of alkanethiols the surface exhibits approximate to 6% of a monolayer of vacancy islands. These results show that complex interactions between the assembling thiols and the herringbone reconstruction influence the mesoscopic aspects of the final monolayer surface.