This is happening when you scan the organization from the Jenkins UI or are you seeing this when webhook fires and starts a scan?
It looks like the underlying issue is that the (external to Jenkins project) GitHub API package doesn't support that webhook event type. We'll need to file an issue with that project: https://github.com/kohsuke/github-api . Filed: https://github.com/kohsuke/github-api/issues/519
As a workaround, you should be able to edit the webhooks for that repo (or the org as whole) and set you Jenkins webhook to not include the "check run" or "check suite" events.
In the links below, edit any Jenkins webhooks to "Let me select individual events".
Please tell me if that works.