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I'm not sure what I should have done differently. I first closed the PR on GitHub, then rejected it here in JIRA (see history tab for details). I then pushed a new PR to GitHub and then added the link to the new PR to this JIRA by updating the workflow.
Looking at GitHub it looks like the correct PR was closed. I'm not sure how GitHub determines if a PR has been merge, perhaps it is just the name of the PR which did not change and GitHub therefor regards it as have being merged.
Either way I'd like to revert the last merge on master and re-open the PR for this task.