I suspect they came up with a process for doing the conversions / redactions that worked for the documents they tested it with, and then applied the process to documents in a slightly different format and just didn't notice. The Verge looked into it and couldn't get a more specific answer than this:

With MIME, the “=” is used to signal either that a string of text should be broken for transmission and rejoined — a “soft line break” — or, when followed by two other characters, that it should be converted to a particular non-ASCII mark.

it doesn’t fully explain why the “=” sometimes replaces letters, like the “J” in “Jeffrey.” No one I spoke to could definitively answer this question, except to say that email is hard and converting it to PDF is harder, and the DoJ was converting a lot of documents in a hurry.

https://www.theverge.com/policy/879016/epstein-files-emails-text-errors-encoding