It does seem like a problem when calling the CGI script. Perhaps you
could debug what cgit is getting from your NGINX?

You could try creating a new file `/var/www/htdocs/cgit/debug.cgi` with
the contents:

    #!/bin/bash
    echo "Content-Type: text/plain"
    echo ""
    printenv

What this script does is: run bash, respond with the Content-Type header
and a plaintext body containing all the environment variables passed by
NGINX.

Give it execution permissions and owned by www-data, then point NGINX to
that script and visit the site. Check the QUERY_STRING, PATH_INFO and
HTTP_HOST and see if they are the correct ones. Is there something strange?

-- 
Ariel Costas (https://costas.dev)
Encrypt your email -- https://emailselfdefense.org/
  GnuPG public key -- https://costas.dev/pgp