I was a bit confused when I read that the command relative_permalinks had been deprecated and as a result I started monkeying with my _config.yml file and the permalink: command (I didn’t mentally register the difference between the two commands). Becuase of my confusion, I was throwing different commands at the config and settled on permalink: /:categories/:title. As a result, Jekyll started creating extensionless links for my posts, which the Jekyll web server handles gracefully. S3, however, doesn’t like extensionless links so the links on my index page — links to individual posts — were broken on S3 because the links didn’t have a trailing slash or an extension.
The solution was to change the permalink command to permalink: /:year/:month/:day/:title/, which is inline with W3’s philosophy of lasting links.