Canonical URLs: How to Disable in WordPress
Canonical URL tags help eliminate self-created duplicate content in the index, which is an important addition to good SEO practices.
In the newer version of wordpress (version 2.9+) they included and canonical URL function. Since any good SEO plugin handles these links in a better format, you can just disable the auto generated one. Adding the following anywhere in your theme’s functions.php will solve the problem splendidly:
# Remove canonical links function remove_action('wp_head', 'rel_canonical');