Automatic ligatures activated, InDesign uses ligatures wherever available. A useful feature in principle, it's effects are in many cases "undesirable" (as Wikipedia puts it in its article on Typographic ligature). Namely "a ligature crossing the boundary of a composite word (e.g., ff in "shelfful")"and this is the case not only in English. In order to get a correct typeset, one has to go through the entire text and eliminate every single wrong ligature by hand.
In English, this may still be doable. In german, there's way more composite than non-composite words. Automation would save a lot of tedious labour. Such an automation would, in my understandig, require a dictionary that that contains those cases (composition borders mostly). It might be structured similar to the one existing in InDesign that contains hints on where to hyphenate. With such a dictionary, I imagine, InDesign could be scripted to turn off ligatures in the particular letter combinations (not entire words) where ligatures are undesired (and maybe even extend the kerningit would be useful to be able to set this 'kerning increment' manually, for different font will require a different increment).
Now, sripting this would be one thing. Getting the dictionary together another one. I was thinking if some exchange platform would be scriptable that allows users to add their ligature exceptions to their 'no-ligatures-dictionary', and then sort of upload their new entries / new version of that dictionary, to fuse it with uploads of others, plus a little forum where all cases of disagreement are displayed and solved?
I know all that, if possible at all, is a bit of labour. But wouldn't it spare much more than it'll cost?