i´ve testet it on more than 10 Domains/Projects. It seems everytime when a canonical is set, eg Easyblog, Hikashop or by Jooomla itself, it generates a second false canonical. A canonical Plugin is not active, i think it must be T4, but i found not the right place to fix it in the code.
The Developer from Easyblog can replicate this, i send you per mail ( alex08@...) the ticket content from the conversation.
If you need a Demo Account on my Server, with this can i help. Naked Joomla3 i can install. Then you can see that when a canonical is set by a component, a second false is everytime set. 🙁
The Hosting Environment is a nginx as proxy, so Apache is used. I think that would not be the problem. But i dont know why you cant replicate..... ive testet it on more than one site, everytime the same and stackideas support can replicate the issue as well.
Ok, let me know, when i can help you.