The accelerating gradient Eacc of X-ray Free Electron Laser (XFEL) prototype cavities manufactured at the industry and treated at DESY demonstrates wide-range scattering from 15 to 41  MV/m. Most cavities satisfy the XFEL specification. Few cavities with low performance (15–17  MV/m) are limited by quench without field emission. The T-map analysis detected quench areas mainly close to the equator. Optical control by a high resolution camera has been applied and allowed to monitor the defects in some cases with good correlation to T-map observation. In order to understand the cause of reduced performance and get more detailed information of the origin of defects, some samples have been extracted from two cavities and investigated by light microscope, digital light microscope with 3D profile measurement, scanning electron microscope SEM, energy dispersive x-ray analysis, and Auger spectroscopy. The electron backscattered diffraction method in a SEM is used to make localized measurements of the lattice curvature. Several surface flaws with sizes from a few μm to hundreds of μm detected by microscopy. The defects can be separated into two categories. The first category of defects consists of foreign elements (often an increased content of carbon). Inclusions with increased content of carbon adhere on the surface and presumably have a hydrocarbon nature. Deviation from a smooth surface profile characterizes the second type of defects (holes, bumps, and pits). Some holes and bumps were found directly in the welding seam. The hot spots in the heat-affected zone (HAZ) of the equator welds have been partially associated with pits too. The study correlates the location of pits with the presence of plastic strain found to remain after welding. Pits near the HAZ were found either coincident with or near areas of high strain. Pits away from the weld were often found at grain boundary triple junctions.