If he had a visa he would have been admitted.
He had an ERFS which is not a visa.
You clearly have no idea what you're talking about.

Presumably the Japanese immigration person didn't have English as their first language.

I am confused where everyone is getting this from. At no point did OP say he had an ERFS document. He said the tour company admitted they produced a visa but they didn't properly file it.

It is fairly easy to deduce for anyone who has been through the process of entering Japan before visa waivers were reinstated.
The tour guide cannot apply for a visa. OP would have had to do this themselves, which they admitted to having not done.
The only possible document a tour company would have provided to them that could have been confused for a visa would be an an ERFS.

Indeed, with entry requirements changing rapidly and being unusual with COVID I have family members that have been denied boarding due to a misunderstanding of entry restrictions by airline personnel. In one case, UA staff at YUL wouldn't accept COVID test results for US entry, but DL did. Maybe that was within the rules, but a bit strange. In the other case, EasyJet staff at LGW would not allow a Dutch passport-holder to fly to France because she wasn't French, despite entry being allowed for EU citizens with a negative COVID test at that time. There were no issues taking the Eurostar. In regards to having issue on attempting to enter Japan again this page (https://www.isa.go.jp/en/application.../kanri_qa.html) sheds some light:
"Q13If I am ordered to depart Japan (via a deportation order), will it be difficult to come back to Japan again?The next time you arrive in Japan, you will not be denied landing for the direct reason of receiving a "deportation order" in the past. However, receiving a "deportation order" means that you did not meet the "conditions for landing." Therefore, you must prove that you meet the "conditions for landing" next time you enter Japan.

The "deportation order" is different from the deportation procedure. Those who have received a "deportation order" will not be denied landing for a period of five years. (However, in cases where the person who received a deportation order due to illegal possession of narcotics, cannabis, stimulants, firearms and swords, or explosives, they may be denied landing permission for a period of one year (Immigration Control Act, Article 5, Paragraph 1, Item 9a.)"

I have been following French rules very carefully and there has never been a time that France admitted EU but not non-EU citizens travelling from the UK, unless the EU citizen was on their way to their country of nationality or residence. They always allowed French citizens in, as they had to, but I and other non-French EU citizens living in the UK were subject to the same rules as UK citizens. As such, it seems to me the easyJet staff were correct.

If the person in question was allowed to travel to France on Eurostar, it will have been in error, or based on an assumption that she was travelling onwards to the Netherlands. Due to the layout of St Pancras station's departures hall, passengers are not normally separated by destination.

Thread closed as things have gone way off track from the original post.

Regards,
armagbedar
Japan forum moderator