WordPress default rewrite rules for permalinks will not work in some cases. For example, when you have some settings declared in htaccess files located in subfolders.
To exclude the subfolders from the WordPress rewrite rules, you need to modify the .htaccess file and change the bold line below:
# 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]