if I put the “.” in the permalink setting to not showing the word “category” in the permalink
That’s not a documented/official feature supported by WordPress. It’s a hack or trick that people use, and it doesn’t work in several scenarios (including paginated archive pages and sub-category pages).
So this is not a “bug” or problem to report.
And I’m sure the smart developers who build the WordPress software have a pretty good reason for adding a prefix in the category permalink. If you want to go against their wisdom and remove the prefix, your only solution is to look for some other trick. Eg most SEO plugins have a feature to remove the category prefix, and there are other tricks out there if you dig in Google.
Good luck!
