My first reaction to this was I bet <link rel="canonical"... has to be in the same domain, but apparently I am wrong - http://googlewebmastercentral.blogspot.com/2009/12/handling-legitimate-cross-domain.html

Done in r76867

Does this also happen when the File-page has a local file page aswell ?

There are many files on Commons that have a mini-page on en.wikipedia with just a {{FeaturedPicture}} template on it.
MediaWiki handles these local filepages without media as a header for the shared image description and is displayed between the .sharedUploadNotice and #shared-image-desc.

Example: http://en.wikipedia.org/wiki/File:NURBS_3-D_surface.gif
This file is on Commons, and description too but it has a local description aswell

I suggest adding another condition to the if statement added in r76867 to see if a local page exists, in that case don't create the canonical link.

I think the check needed for that would be: this->getID() == 0

I have no real preference either way, what do others think ?

<link rel="Canonical"> only works (from my understanding) if the pages are the same, or very close. If a wiki created a local description page, the description might not be close enough for the link tag to work.

But assuming the <link rel="Canonical"> actually works in that case, then we would be stopping content on the local wiki from being indexed, which seems wrong.

Done in r76999