There are numerous posts on  errors encountered post enabling permalinks , especially  when wordpress is in a subdirectory.

 

Please add following code in your main virtualhost  to fix this up. Use of .htaccess is not recommended if you are using Apache (Source : Apache)

 

<Directory "/home/user/blog">
      RewriteEngine On
      RewriteBase /blog/
      RewriteCond %{REQUEST_FILENAME} !-f
      RewriteCond %{REQUEST_FILENAME} !-d
      RewriteRule . index.php [L]

      Options FollowSymLinks
      Order allow,deny
      Allow from all
    </Directory>

Here "/home/user" is the root directory of main website and "home/user/blog" is the directory of blog
Resolve 404 error in wordpress post enabling Permalinks
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