“Oops.” error on an html file directly uploaded to a subdirectory of my WordPress site

I can see the index of /files directoy and prototype-pivot-pong/boilerplate.html doesn’t exist. So, the 404 error is correct.

Also, you must know that, if the requested URL hits the directory of WordPress and it doesn’t match a real file, the request will be handle by WordPress, at least you set your own RewriteRules in .htaccess above WordPress RewriteRules.

For example (not tested, just written here as sample):

RewriteRule ^files/prototype-pivot-pong/boilerplate\.html$ /files/index.php?file=boilerplate [L]
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>

EDIT

You say that the directory exists in your server but you can not access to it using browers. In that case, try to check permissions. If the directory and files are there and are accesible for public (for example, 755 for directory and 644 for files), they should be accesible in browsers. You can also contact with the support of hostihg company if the problem persists, I think it is not related with WordPress at all.