What you’re reporting is not the default WordPress behaviour. And you seem to be mixing up two things here: post permalink vs category permalink.
Permalink Custom Structure: /category/%category%/%postname%/
https://example.com/category/category-name/
https://example.com/category/category-name/page/2/
That’s not default WordPress behaviour, unless you’re doing something else elsewhere.
With the custom permalink structure: /category/%category%/%postname%/
Post permalink should become example.com/category/category-name/post-name/
While category permalink becomes: example.com/category/category/category-name/
Note the double category
in the category permalink. This is because WordPress automatically adds the category
base to category permalinks, so there’s no reason to include this again in your permalink structure.
But when I use prefix ‘.’ and Permalink Custom Structure: /%category%/%postname%/
this works:
https://example.com/category-name/
but this returns 404
https://example.com/category-name/page/2/
Again, the custom permalink structure /%category%/%postname%/
should NOT, by default, produce these URLs you’re reporting. Instead, you should get:
Post permalink: example.com/category-name/post-name/
Category permalink: example.com/category/category-name/
… and these should not return a 404 error on paginated pages.
If you’re indeed getting the URLs you’re reporting, then something else may be going on.
My guess: you (or a plugin you’re using) may be removing the category
base that WordPress automatically adds to category permalinks. This is a common cause of 404 on various archival-type listings.
If you can give your actual domain name, I could dig deeper into this for you.