The system should mark a pull request as merged if the commits in it are merged into the destination branch manually, even if the 'Merge' button was not clicked on the website. It looks like that is what happened here.
Hmm, thanks for the clarification. I will dig deeper into this.
Looking at the history of the pull request, it looks like when it was created, the tip revision on the source branch was 03cb085e2c5e (which doesn't seem to exist anymore in the jashar86/gazebo fork), and on 2012-10-18, user 'nkoenig' updated it to use add7700a919f as the tip. add7700a919f is the revision I linked to above, which is already in the destination repository (osrf/gazebo).
The really strange thing is that the change attributed to 'nkoenig' on 2012-10-18 is marked as being an 'internal' update to the pullrequest, which means that the system made the update in order to maintain data integrity. Was the jashar86/gazebo repository stripped around then?
The replacement pull request you linked above has a different commit, 59a4454. Is that meant to be the exact same commit that should have been in the original pull request, or did the developer re-create the fix, and open a new PR?