Directory outside Wordpress delivering 404 -- just on subdomain - php

Question

I have a very basic Wordpress install, with WP in root and permalinks on. For external directories I set up, things are working fine, no matter what's in them.
BUT, I recently replicated the site on a subdomain, to use as a dev site. That site has its own files, and its own database. On it, any php files in external directories are resulting in a WP-served 404 error. It serves html files within those directories just fine.
To recap:
mysite.com -- Wordpress site, all is fine
mysite.com/kitties/file.html --> html file outside of WP, fine.
mysite.com/kitties/file.php --> php file, outside WP, fine.
dev.mysite.com --> Wordpress site, all is fine
dev.mysite.com/kitties/file.html --> html file outside of WP, fine.
dev.mysite.com/kitties/file.php --> php file outside of WP, returns WP-served 404
My .htaccess file is below, and standard, but given that the problem is only on the dev site, I don't know that it has anything to do with htaccess, and wonder if it's an apache configuration issue?
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress

Answer 1

When Moving / duplicating a site it is usually wise to resave the permalink settings, even when nothing changes.
Did you change the url in the settings of wp-config?
After that it is also wise to check the database for urls (tool).
Try those and see if the problem still exists.