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Well, the title question says it all I think:
A footnote refers to the wrong document - what is a word to describe this kind of mistake?
Words like "discrepancy", "incongruence", "fallacy", or simply "mistake" may be fine, but I am presuming this specific kind of error has its own terminology.
Mistake is fine, but typographical error. might be better:
a mistake (such as a misspelled word) in typed or printed text
This makes it clear that it's likely a mistake as a result of writing the information down, rather than with methodology, or logic, or something else.
