I think we have a terminology issue here. The visa is not "filed with the correct authorities" - it's issued by the correct authorities. It sounds to me that they filled out the visa application but did not (fully) submit ("file") it. A properly filled out but unfiled visa application is not a visa that's not filed with the correct authorities - it's not a visa at all. It's kind of like filling out an application for a passport but then forgetting to send it into the State Department: a copy of your application isn't a "passport not filed with the correct authorities" - it's not a passport at all in any sense of the word - it's just an application for one that was never filed properly. I think my guess here is correct, as I can't think of any other set of circumstances that would be consistent with what you said above.

This is such an unfortunate set of circumstances, and I'm sorry to hear it. It sounds like you did everything you thought you needed to: you first contacted the consulate, who told you you needed a Japanese tour operator to arrange for things. You did so, and relied on them to do the paperwork, not knowing the distinction between an ERFS certificate and a visa. And, the airline didn't catch it. Had you been following the thread here on FT on such matters, you probably would have caught it, but you were probably doing more important things, like saving your patients' lives.

As a point of order, he was refused entry, not deported. Deportation happens after you're admitted (or otherwise get into the country illegally). The question on the arrival card does ask "Any history of deportation or refusal of entry?" so in that regard it's moot case, as you'll always have to answer Yes to that question. But any affect on future admissibility that apply to people that have been previous deported would not apply to this situation unless they also apply to people that have been refused entry. I don't know how Japan works in this regard, and "contact the consulate" is probably good advice in this case, even though I think that advice can be overused in some other situations.