htaccess rewrite, how to negate sub directory files - .htaccess

Question

I have htaccess file performing URL rewrite. It basically removes the .php extension.
The rules work fine, e.g. they successfully rewrite http://example.com/contact.php into http://example.com/contact
However the rewrite also changes sub directory files, such as /includes/check-form-input.php.
So when, for example, a form at contact.php attempts to submit to /includes/check-form-input.php the htaccess rewrite strips the .php from the end and I get 404 headers.
i.e. /includes/check-form-input is not found.
At least that's what appears to happen, using HTTP_REFERER seems to confirm this as the referer was /includes/check-form-input without the ext .php
Is there a way to add a rule to negate all sub dirs?
I have the following htaccess - which is copied from another answer here on SO, as I don't 100% grasp the rewrite structure.
(I've left in the www to non-www redirect in case it's the cause)
## Rewrite on
RewriteEngine on
## Redirect all pages from non-www to www
Options +FollowSymLinks
RewriteCond %{HTTP_HOST} ^www\.example\.com$ [NC]
RewriteRule ^(.*)$ http://example.com/$1 [R=301,L]
## URL rewrite
# Unless directory, remove trailing slash
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^([^/]+)/$ http://example.com/$1 [R=301,L]
# Redirect external .php requests to extensionless url
RewriteCond %{THE_REQUEST} ^(.+)\.php([#?][^\ ]*)?\ HTTP/
RewriteRule ^(.+)\.php$ http://example.com/$1 [R=301,L]
# Resolve .php file for extensionless php urls
RewriteRule ^([^/.]+)$ $1.php [L]

Answer 1

You can either exclude all subdirectories,
# Redirect external .php requests to extensionless url
RewriteCond %{THE_REQUEST} ^(.+)\.php([#?][^\ ]*)?\ HTTP/
RewriteRule ^([^/]+)\.php$ http://example.com/$1 [R=301,L]
or limit it to only GET requests:
# Redirect external .php requests to extensionless url
RewriteCond %{THE_REQUEST} ^(GET|HEAD)\ (.+)\.php([#?][^\ ]*)?\ HTTP/
RewriteRule ^(.+)\.php$ http://example.com/$1 [R=301,L]
or just exclude the includes subdirectory
# Redirect external .php requests to extensionless url
RewriteCond %{THE_REQUEST} ^(.+)\.php([#?][^\ ]*)?\ HTTP/
RewriteCond %{REQUEST_URI} !^/includes/
RewriteRule ^([^/]+)\.php$ http://example.com/$1 [R=301,L]