I believe this is an issue on the Medium side. I am seeing this canonical link in the source of the linked article:
<link data-rh="true" rel="canonical" href="https://gist.github.com/139a99b16e8d1fb37b1b3634b14d9052"/>
Onebox library always follows the canonical link.
Other Medium articles are oneboxing fine so it might be a regression in Medium articles with Gist embedded.
We can add medium.com to the list of domains to ignore canonical tag, should we do that @sam? Note that Medium allows custom domains so this will not work in all the cases.