To remove a user from a site you need to click on the change button on the right side of the user’s row. In the dialog that shows up, you’ll see a list of sites the user has access to, along with his access level. Click on the trash can icon to remove the user from the appropriate site, then click confirm to finalize.
You can also remove multiple users from a site at once. To do this, first, use the site filter to filter the list to users with access to a particular site. Then select the users you wish to remove using the checkboxes on the left. Finally, click on the remove button in the top-right side of the table and select the “remove from site” option. A dialog will show up where you’ll need to click the remove button to finalize.