List with filtered open PR on the API is different from the website

While using the GitHawk app I found a filtering issue related to the GitHub API. When I filter my PR’s on the website to is:pr is:open it shows the correct list. But when I do this via the API and using 

repo:[repo name] is:pr is:open it shows an old merged PR in the list. When I enter this exact line on the GitHub website in the PR filter, it shows the same old merging PR.

This is what the API returns in the JSON file:

{
	"__typename": "PullRequest",
	"createdAt": "2018-12-05T18:36:39Z",
	"author": {
		"__typename": "User",
		"login": "***"
	},
	"id": "***",
	"labels": {
		"__typename": "LabelConnection",
		"nodes": []
	},
	"title": "Fetch Classes: Addition Filter Date Parameters",
	"number": 19,
	"pullRequestState": "MERGED",
	"commits": {
		"__typename": "PullRequestCommitConnection",
		"nodes": [{
			"__typename": "PullRequestCommit",
			"commit": {
				"__typename": "Commit",
				"status": null
			}
		}]
	}
}

It’s related to a Repo at work, so can’t share more data to the public but I created an X-GitHub-Request-Id with the request that returns this data: CE5C:4F95:18A781D:3BCA0EF:5CE44C4D

For privacy and security reasons, we don’t have access to private account details, including information in private repositories. Because of this, we can’t investigate what might be going wrong with this particular PR or repository. If you can reproduce the problem in a public repository, we can take a look. Or you can contact private support at https://github.com/contact and they can take a deeper look into what’s going on.

I hope that helps!

The problem has been solved. GitHub dev support triggered a re-indexing for the repo. Another work around is to add a label and remove that label to close the PR properly.