We present an ultra-high vacuum scanning tunneling microscopy (STM) study of structural defects in molybdenum disulfide thin films grown on silicon substrates by chemical vapor deposition. A distinctive type of grain boundary periodically arranged inside an isolated triangular domain, along with other inter-domain grain boundaries of various types, is observed. These periodic defects, about 50 nm apart and a few nanometers in width, remain hidden in optical or low-resolution microscopy studies. We report a complex growth mechanism that produces 2D nucleation and spiral growth features that can explain the topography in our films.