1) Try printing the wp_upload_dir()
function in one of your templates so you can see what's going on under the hood:
<?php print_r(wp_upload_dir()); ?>
This output an array that looks something like this:
Array ( [path] => /root/of/site/wp-content/uploads/2016/07 [url] => http://whatever.com/wp-content/uploads/2016/07 [subdir] => /2016/07 [basedir] => /code/wp-content/uploads [baseurl] => http://whatever.com/wp-content/uploads [error] => )
2) If that path is wrong, you need to reset it. Check in your wp-config.php
and see if you are redirecting the default download folder to something custom. Look for this line of code:
define('UPLOADS', 'custom/path/here');
If you don't see this line of code, put it in there and set it to whatever you want.
3) You can override the behavior you are seeing with plugins. My favorite is called Custom Upload Dir: https://wordpress.org/plugins/custom-upload-dir/. Search around a bit, there are a number of similar plugins for you to try.