Hi,
This is what i have done now to fix the errors.
The following line
echo '<link rel="canonical" href="' . esc_url( $canonical, null, 'other' ) . '" />' . "\n";
is converted to
echo '<link rel="canonical" href="' . esc_url( urldecode($canonical), null, 'other' ) . '" />' . "\n";
And I have added
$url = urldecode($url);
to the next line of
$url = $this->canonical( false, true );
I am not sure it is a right solution as it touches the core of plugin. Anyway, it works for site.