I wonder if at some point your e-book went through macOS's Preview program.
At work I sometimes have to copy blocks of text from a PDF into another document. If I do it with Preview, I lose the fi and fl ligatures. It only happens with PDFs created in-house, so I guess it's some kind of stylistic thing that comes from the guy who lays out the PDFs.
I eventually learned to use Adobe's own Acrobat, instead, and it works fine.