Sometimes the default WordPress rewrite rules might not work for permalinks. E.g. If you have other configurations declared in .htaccess files placed in sub-folders.
You must edit the .htaccess and need to change the bold line below to omit the sub-folders from the WordPress rewrite rules.
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress
To
RewriteRule ./ /index.php [L]