Just when you thought things couldn't get stranger ...
Here's an example of an fi ligature turning up
in a footnote of a sideloaded AZW3 book. I've checked the source epub and it is definitely not hard-coded. I exploded the converted AZW3 and it's not hard-coded there either. Unfortunately so far I've been unable to replicate this in a test book.
(The book was passed through Hyphenate This! which explains the first word.)