double canonical tag

Extensions that create their own canonical tags are ignored by route66 plugin.
several lines of code added to the system/route66 plugin fix the issue.
From the comment, I added 8 lines.  Then I added one test to the addHeadLink test (&&empty($canonical))What this modification does is check the head links for an existing canonical tag.  If it's empty - your route66 generated canonical tag is added.
public function onBeforeCompileHead()
{
$application = JFactory::getApplication();
$document = JFactory::getDocument();

if ($application->isClient('site') && $document->getType() == 'html')
{
// Check if a canonical html tag already exists (for instance, added by a component).
$canonical = '';

foreach ($document->_links as $linkUrl => $link) {
if (isset($link['relation']) && $link['relation'] === 'canonical') {
$canonical = $linkUrl;
break;
}
}

if ($this->params->get('canonical', 1) && $this->canonical && empty($canonical))
{
$document->addHeadLink(htmlspecialchars($this->canonical), 'canonical');
}

if ($this->params->get('facebookPageId'))
{
$document->addCustomTag('<meta property="fb:pages" content="' . $this->params->get('facebookPageId') . '" />');
}

if (JPluginHelper::isEnabled('content', 'route66metadata'))
{
$this->setMetadata();
}
}
}

No, I'm not using another extension to generate canonical links - one of the extensions I use (a component) generates its own canonical links for pages generated by that extension.  It's not sitewide, just one menu item does this.
The Joomla SEF plugin can also generate canonical links if it detects that one is not already present.  I adapted the Joomla SEF plugin code to your extension, so yours does not generate canonical links when something else has already done it.