Why does this twilight sky flat field have a grid of dark pixels?
Yes, it's some sort of CCD structure originated from the manufacturing process. CCD chips with large area were produced by chunks of several hundred pixels. see http://heasarc.gsfc.nasa.gov/Images/astroe/about/xis_config.gif

And sometimes position offsets between these chunks can be detected.



from Wilken et al., 2010, MNRAS, 405, L16