Drupal multi site 404s, sub directory site subpages going to default site
You didn't mention anything about sites.php, so I'm going to guess that's where the problem resides.

Google it: https://www.google.com/#q=drupal+multisite+sites.php 
D7 example: https://api.drupal.org/api/drupal/sites!example.sites.php/7.x 
D8 example: https://api.drupal.org/api/drupal/sites!example.sites.php/8.2.x

Please post your sites.php file if you're unable to fix the issue after taking a look.