I make a PR from my fork to the upstream branch, I also merge the PR.
In this case there is only one commit in the PR. After the PR is merged and I look at the commit history of the upstream branch I see this : 
Why is that? For me it looks a little confusing that there is an entry for both the commit and the PR. I am sure I just don't get why it is like that :)
It sounds like a pretty straightforward pull request and merge.
Maybe you're confusing it with a rebase. This article is quite helpful. Or is there something more to your question I'm missing?