It wasn't a horror story but a simple fact that it was layer of complexity that wasn't really helpful at all.
When code volume was small, nobody noticed, and hey "it looks nice". Some time after though, when volume increased it started to get really burdensome. I used this as a part of Rails pipeline, so it was like: write some coffeescript, compile, run - something failed - usual process.
However the code was already mangled, often source code mapping didn't want to work. When source code was found it wasn't uncommon that it caused by operator precedence or code not transpiled in a way it was intended and requiring debugging transpilation process.
At some point I suggested to migrate away from CoffeeScript toward (almost plain) JavaScript and most developers happily agreed to that. We were able to migrate big chunk automatically, rest took only few weeks to clean up. Velocity increased and people were happy they don't have to deal with it anymore.
Ultimatelly it is the truth with most of the transpilers - sooner or later you get into idiosyncracies that - if technology is not popular enough - you're left alone to solve.