If anybody wants an example of where ligatures will cause problems, try playing a roguelike in a console using the Fira Code font with ligatures turned on. It demonstrates that accidental collisions end up with completely different glyphs. My first experience with this was with Dwarf Fortress in text mode.

But... I have to say that this is the only place I've actually come across it. I eventually decided that I don't like ligatures, personally, in my source code. However, the chance of problems occurring is pretty remote.