Repeating rel="canonical" code

Could you please advise how to fix this bug? All content analysis programs complain about it. Sometimes, for unknown reasons, the canonical URL becomes /vasya upon saving, and other times it's index.php/petya, for example. The Metatag module is installed. I didn't set anything unusual in the configuration. For now, I’ve blocked all pages like /index.php/v* in robots.txt. Could you tell me if that was the right thing to do?