Nothing is more annoying than having to manual search a document that has been exported from PDF and have to make sure you catch all the now incorrect spellings when all the ligatures have just disappeared "action" -> "ac on", "finish" -> " nish".
As far as I understand, PDFs can be generated such that ligatures can be correctly cut'n'pasted from most PDF readers. I have seen PDFs where ligatures in links (ending in ”.fi”) cause problems, and I believe that's just an incorrectly generated PDF; ligatures done wrong.
Considering that PDF a programming language designed to draw stuff on paper, going backwards from the program back to clean data is not something that one should expect to always work.
I play (tabletop) RPGs online, we use a simple, free rule system (Tiny Six) and any time that I have to copypaste a specific paragraph of the rules in chat I always discover that there are missing characters (so I have to reread the block and fix it, ... in the end it would be faster to just read it aloud in voice).
Same might happen with scene or room descriptions taken from modules etc.
This is assuming you cleaning up the output of `pdftotext` which in my experience is the best command line tool for extracting plain text.