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Subdirectory multisite subsite links not working

We have a multisite using subdirectories.

In www.example.com/site1 if I click on contact, it should go to www.example.com/site1/contact/ however, it goes to www.example.com/contact/.

This is the .htaccess in /public_html, from this example:

RewriteEngine On
RewriteBase /
RewriteRule ^index.php$ - [L]

# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) $2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*.php)$ $2 [L]
RewriteRule . index.php [L]

Help appreciated.