Apache incorrect url rewrite for non-existent symlink files

I have a directory (foo/uploads), which contains 1 file: file1.txt

I have created a symlink to this directory (bar/uploads)

Here is my .htaccess file inside bar:

RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^ index.php [L]

And this is my vhost file:

<VirtualHost *:80>
    ServerName bar.com
    DocumentRoot /var/www/bar

    <Directory /var/www/bar>
        allow from all
        order allow,deny
        AllowOverride All
    </Directory>
</VirtualHost>

The problem I'm having is, if I try to access a non-existent file when using the symlinked folder, it is not producing a 404 response. Here is what I mean:

1. foo.com/uploads/file1.txt -> file served (CORRECT)
2. foo.com/uploads/file2.txt -> Apache 404 ErrorDocument served (CORRECT)
3. bar.com/uploads/file1.txt -> file served (CORRECT)
4. bar.com/uploads/file2.txt -> proceeds to index.php (INCORRECT)

I have also tried including:

RewriteCond %{REQUEST_FILENAME} !-l

Before the RewriteRule, but that doesn't make a difference.

Anyone know what I need to do?

If you only want the front-controller to apply when accessed via bar.com then you could check the requested Host header in the rule. For example:

RewriteCond %{HTTP_HOST} (^|\.)bar\.com [NC]
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^ index.php [L]

Or, exclude the /uploads subdirectory:

RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule !^uploads/ index.php [L]

Or, include another .htaccess file in the /uploads subdirectory that overrides the parent front-controller pattern. You can do this simply by disabling (or enabling - providing mod_rewrite inheritance is not enabled) the rewrite engine in the subdirectory:

# /uploads/.htaccess
RewriteEngine Off

Alternatively, disable .htaccess overrides altogether and move these directives to the <Directory /var/www/bar> container inside the bar.com vHost.