I have noticed similar. The Sigma 13k Select II does indeed scratch the bevel, not unlike natural stones.
If you are interested, I am working on a review regarding the Sigma Select II 13k and can provide some images I made for comparison.
The Naniwa SS8k and SS10k provided a very high grade mirror. I dare say this mirror will only be outperformed by industrial grade 3M lapping film.
So far I tried Shapton Pro, Shapton GS, Naniwa Chosera, Suehiro Gold and the above mentioned Sigma 13k. None of them came close to the Mirror of the SS.
Here is a picture of a bevel set with 3M lapping film. The progression was 5µm silicon carbide, 3µm aluminium oxyde, 1µm aluminium oxyde and for good measure 1µm diamond lapping film.
That is what the bevel and edge looked like
Attachment 91246
Magnification ~40x. Almost impossible to focus on. I used different angles and light settings, always the same result
Attachment 91245
Magnification ~120x. The edge looks flawed, but it is not! The distortions are halos from the camera and lighting.
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This polish has been set with a constant sharpening direction. All scratches from the lapping film where in the same direction (and have been removed completely, anyway).
The Sigma Select II 13k I used with a different sharpening direction! 40 laps have been done in the direction from top left, to bottom right of the image, whereas the bevel setting has been done in the opposite direction.
I finished with 20 laps perpendicular to the edge. The only source for all scratches in these directions is the Sigma 13k. There was no possibility of "underlying scratches popping up" (a theory I do not subscribe to).
Attachment 91248
Magnification ~40x. There are more pictures with different light settings, all show these scratch marks
For the final test of the edge, I executed a micro bevel with a second layer of tape. The resulting edge was fairly straight and only slightly jagged at this high rate of magnification.
The edge was similar to that of the Shapton GS 16k and better than Naniwa SS10k.
Attachment 91247
Magnification ~120x
Now, to the naked eye the polish does look good. Depending on the angle of light you may get a very dark luster but if you are looking for it you will find the scratches as fairly thin white lines with the naked eye.
The loupe will reveal these quickly. If you are not striving for the perfect polish, the Sigma 13k may be interesting for you! The Shapton GS 16k produces similar results; to the naked eye the luster is impeccable (thus slightly better than the Sigma 13k). But the loupe will reveal even thinner and more shallow white lines.
Under magnification you will get something like this:
Attachment 91250
Note this is a different razor (with a much smaller bevel), different light settings and a different stone!
So these images are not really comparable