New Site Loads But Appears Broken

Symptoms after Cloning:

• The new cloned site looks messed up
• Missing images
• Broken stylesheets
• Broken javascript
• Site using incorrect theme
• 404 errors in the Browser Inspector

Cause and Solutions:

That can be caused by several things – something unrelated to the Cloner:

1. Most likely cause: object caching on your server. Try clearing the cache via your hosting control panel.
2. Second most likely cause: Incorrect .htaccess file that is not providing correct multisite paths for subsites. More common on multisite networks using the subdirectory structure like yours. Search on wordpress codex htaccess and make 100% sure your htaccess file is identical to the one WordPress provides for subdirectory mode in multisite.
   
   You can confirm that this particular cause is the most likely culprit by looking in your browser’s inspector (right-click > Inspect Element) and examining the dropped resources. They will likely be a combination of images, CSS, and JS. The URLs that the site is looking for and cannot find (thus generating 404 errors) will match the pattern: https://yourdomain.com/newsite/wp-content/filepath 
   
   Please see this link for more information and try updating your .htaccess file to the correct one for multisite (using the Subfolder Example): https://codex.wordpress.org/htaccess#WordPress_3.5_and_up
   This is not a Cloner issue but a multisite configuration issue.
3. Non-standard / custom setting in the subsite option for uploads path and uploads dir. Check your subsites wp_options table (you can also look at the values under wp-admin/network > sites > all sites > [hover on the site name] > edit > [Tab] Settings > search the page for the fields with “upload” in the name… there should be a couple of them and they should both be BLANK. If you were using a custom structure in those fields for your main site that you cloned, then you might have to do some shuffling of files / settings.
4. Thumbnails need to be regenerated and/or file permissions reset.
5. Uncommon, but possible: corruption in MySQL and/or bad values for the references to those files.