Topic won’t save for a custom post type — how to debug?

I don’t know of any “default” “topics meta boxes” in WordPress. Have you switched to a default WordPress theme to see if this still shows up? Sounds like theme, or some other plugin is adding that (post a screenshot to help us … help you).

You should do a search in folder (using whatever IDE you have) looking for a string, or something else you see on the screen for the “topics” that way you can pinpoint who/what is adding that (even if it is core).

Chances are it’s using either save_post_{$POST_TYPE} or save_post hook to update any custom meta or other values … but even then without knowing “where” the “topics” is coming from it’s hard to say.

You can get a free/trial copy of PHPStorm EAP (Early Access Program) from here:
https://www.jetbrains.com/phpstorm/eap/

Setup xDebug handling and add a breakpoint and literally walk through your code until you find the issue. Will save you hours of time, not only now, but in the future as well.

You can also use Local by Flywheel to setup a local WordPress installation and they have an addon to automatically setup xDebug in PHPStorm.