Aimy Canonical v3.9.0 PRO allows to automatically clean up unnecessary canonical link tags from <head>!
Cleanup <head>
Under some conditions, multiple canonical link tags may be inserted into your pages' <head>.
For example, it may be the designer of your Joomla! template inserted one as well as a SEO extension you have installed on your website, without using Joomla!'s mechanism for handling links in a page's <head>. If this is the case on your website, just enable this option and Aimy Canonical PRO will clean up any canonical link tag from your <head> automatically and insert a single one at the end of the page's <head> afterwards.