Hi,
It seems that on Joomla 3 the System - SEF plugin automatically generates the canonical link in addition to JoomSEF.
Unfortunately, currently the only solution is to either disable the System - SEF plugin if you don't need it, or modify its source code. In case you want to do the modification, follow these steps:
1. Locate the /plugins/system/sef/sef.php file on your web server
2. IMPORTANT: Backup the file!
3. Edit the file in a text editor
4. Find the following lines:
if ($uri !== $link)
{
$doc->addHeadLink(htmlspecialchars($link), 'canonical');
}
and change them to:
if ($uri !== $link)
{
//$doc->addHeadLink(htmlspecialchars($link), 'canonical');
}
That way the standard canonical link from Joomla won't be generated.