Let’s Encrypt’s staging environment currently makes multiple HTTP requests from multiple ISPs. (Currently from different data centers at 2 ISPs, but that is not guaranteed, and it’s sure to change in the future.) In your HTTP log, there isn’t a request from the most important one. So it’s seemingly true that it failed for some reason.
IPv4 routing issues between Let’s Encrypt and Linode in Newark would be surprising, but anything’s possible on the Internet…
fail2ban, perhaps?