I have two images shown below. Same calibration masters used on both of them. On the left is an image that was taken (I later determined) through high clouds. On the right an image through a relatively cloudless sky. Same exposure duration in each of the image subframes.
What I'm curious about is why the cloudy tainted data show strong edge artifacts (top, right, bottom edges), while the cloudless images show no such artifacts. Indeed, if you examine the residuals of the flat field master, after removing the overall dome, you see edge features just like seen in the image on the left.
So, why do you think that cloudy tainted data bring out those faint master flat artifacts?