OK guys, I did not know this was such a big issue until today.
Appearently SP add's a rel="canonical" to every SP website that uses a custom domain (= most of them). But as we all know Google only accepts rel="canonical" tags when there is maximum 1 in the code. Because SP is adding its own code that means we can not add our own rel="canonical" tag to avoid duplicate content.
In a current project I have this problem, because we have duplicate content and the canonical website is of course a SP website.
I hope there is someone with a solution on how to bypass or override the default rel="canonical" tag in SP.