He needed two tickets - The basic fare ticket and the express train ticket. He only had the express train ticket, so the ticket gate did not let him through.
https://www.jreast.co.jp/multi/en/ticket/types.html

Possible explanations are 1) the machine failed to print both tickets, or 2) the machine did its job but he failed to collect and retain both tickets. [EDIT: or 3) he purchased only the express ticket without a basic fare ticket]. Judging from the video, I doubt that he can tell you which of these occurred. My money is on the second explanation.

The agent at the ticket office communicated adequately with the assistance of a translation app and sold him the basic fare ticket that he needed. If that is terribly worrying to you, I suggest that you stop watching videos by people who say "the signs are all in Japanese" in a wobbly voice, as they walk through a station with multilingual signage and electronic displays that switch between languages.