moving to InDesign forum for assistance
What happens when you create a PDF from the original InDesign file?
If I open the original InDesign document in CC2015, no matter what I do with
it the ligatures are there! Including; Making PDF's exporting IDML's and
printing postscript. It's embedded in the file as a change or modifications
would be. If I open the client supplied IDML in a lower version of InDesign the
file is fine no matter what is done to the file. There are a couple of other
posts on the site where the user has performed a great deal of tests and the
conclusion was to issue a support ticket to adobe as a bug. If you search this
forum for ligature problems you will see many reports of the same thing. I did
find one from a print service provider where an MVP took a user thru rounds of
tests and the conclusion was to open a support case with adobe.
To my knowledge the only solution in CC2015 would be to manually locate the ligatures and manually turn them off.