Custom post type slug not working properly, 404

I have two custom post types notes and programs, one custom taxonomy called subjects attached to them.

I want to achieve following:
For notes: https://site.com/%subject%/note/%postname% (https://site.com/data-structures/note/bubble-sort-algo)
For programs: https://site.com/%subject%/program/%postname% (https://site.com/programming-in-c/program/hello-world-in-c)

On my WCK settings page,
WCK Rewrite Slug: %subject%/note for notes and %subject%/program for programs.

I’m using Custom Post Type Permalinks plugins. Without it, %subject% is not working.
In the Permalink Settings page, settings are as below:
common setting:
post name i.e. https://site.com/%postname%/
Permalink Setting for custom post type: (square braces are editable text input)
note – https://site.com/%subject%/note/%postname%
program – https://site.com/%subject%/program/%postname%

Now, https://site.com/data-structures/note/bubble-sort-algo and https://site.com/programming-in-c/program/hello-world-in-c are showing correctly but my main post are giving 404 (https://site.com/post-name). Even pages are also giving 404 (https://site.com/about).

Whats the matter?

https://www.ads-software.com/plugins/wck-custom-fields-and-custom-post-types-creator/