WordPress site in subdirectory load site in main directory

There are some things you can try:

  • Check the wp-options table in your staging site database and look for
    site URL in 2 places. Change it to the correct staging address if already not.
  • Refresh the permalinks of the staging site.

I am guessing this should fix your problem. If not, please share your website address.

P.S. If both the sites (main and stage) have the same content, you might wanna add a robots.txt file in the staging instance just to be safe from being considered as duplicate content.