There are two main root causes of payload delivery timeouts:
networking issues. The GitHub server cannot reach the drone server.
webhook address is incorrect, which means you probably have an issue with your drone configuration. This is especially true if you are running drone behind a reverse proxy.
You will need to look at the webhook URL in GitHub and verify the address is correct. You will also need to verify the webhook address is accessible from your GitHub instance.
This GitHub error message is also displayed when there is no .drone.yml (accidentally removed in a pull-request)
Just the logs give some insights
time="2018-06-19T11:20:27Z" level=error msg="error: user/repo: cannot find .drone.yml in refs/pull/6/merge: GET https://api.github.com/repos/user/repo/contents/.drone.yml?ref=94c3c20f35????a3d1eb14658f691????e19c12cd4: 404 Not Found []"