I suspect there's a common issue in a lot of martial arts. I'll use NGA as an example.
We know who the founder was (Morita Shodo), the approximate time the art was founded (I'd have to look in my notes for that, but early 1940's I think), and the lineage to the current head of the art (Richard Bowe trained under Morita for years until his death, kept in touch with his successor until he retired). Beyond that, we have bits and pieces. Who did Morita train with in Daito-ryu? We think it was Kotaro Yoshida. We have no documentation of that, and since the passing of Nara Tominosuke (the second head of the association, and Morita's step-son), we have no real detail. Mr. Bowe wasn't very focused on history when he trained (neither was I), so he didn't really ask a lot of those questions. He was focused on the efficacy of the art. Official records for Daito-ryu appear to have been fragmented when lineages split up. And apparently it wasn't uncommon to use different names for some things around that time in Japan, so if Morita is in the records, he might not be under that name. And apparently some instructors taught without entering folks in the Daito-ryu rolls.
Put all of that together, and even with a fairly recent art, there's a disconnect. Record keeping was not the same in the past. Some styles kept no records (I'd be surprised if that weren't at least partly true of FMA). Written records were passed along from one person to the next, and could be lost if someone died without passing theirs along, if there was a fire, etc.
In some cases, historical research in MA has more in common with archaeology.