>>3394247Yeah, those happen almost all the time. You have to edit them out by finding and editing the mask layer that corresponds to the best in-focus image. Compound that by how much RAM having 25-100 images layers open at once takes up and trying to edit them. The process can take hours sometimes. Generally, the easiest way to remove those lines around the boarders is to keep them in mind when composing then cropping the image to remove them.
The more difficult problems are from occlusion. As the lens focuses, the rail moves, or the bellows moves the perspective of the lens element changes. Anything that blocks then reveals a portion of the subject, as you take photos for focus stacking, often times ends up with blurry outlines after focus stacking. Insects with whiskers and hairy sections are the worst times this happens. The more magnified the lens is the worse this can get since the working distance is so close and thus the perspective angle changes by a wide margin between images. Fixing it by hand can be maddening.
>7:1 example of occlusion problems with focus stacking, note the hair sections. 
