How to debug a 404 error on pages whose content is perfectly displayed when I explore it?

Question

I have this issue I can't understand : recently (everything was working perfectly during years), some pages on my website are returning a 404 error while I can perfectly access to their content (even after removing any cache).

It's only "Third level" pages of a Custom Post Type : First level return 200 status code -- Second level page return 200 status code ----- Third level page return 404 error

Actually I only have this issue on a hierarchical Custom Post Type whose "CPT Base" I have removed.

When I go on the Dev Console from my Browser, I can see the 404 error even if the html with all the content is perfectly fine.

I try to reproduce the bug on a new install with the same plugins, content, and I have a 200 status code.

What am I missing ?

Here you have an example of these pages maybe it would be more clear : https://polesupnature.fr/btsa-gpn/programme/biologie-ecologie/

Here is the HTTP Header I get and the content is still returned perfectly… :

HTTP/2 404 
date: Wed, 16 Nov 2022 15:38:54 GMT
content-type: text/html; charset=UTF-8
server: Apache
x-powered-by: PHP/8.0
expires: Wed, 11 Jan 1984 05:00:00 GMT
cache-control: no-cache, must-revalidate, max-age=0
link: ; rel="https://api.w.org/"
link: ; rel="alternate"; type="application/

Answer 1

Actually, the issue came from the Remove CPT Base plugin. It is a solved problem now. The plugin author gave this explanation about what caused the 404 error :

I used pre_get_posts hook to convince WordPress that it should load specific content on specific URL, but 404 headers were already sent, so I had to use another hook that fires before sending headers – request hook.