Something unintelligible is difficult to understand, either because the room is too noisy or because the unintelligible thing is too quiet or confusing.
We use our intelligence to understand things, and something intelligible is easy to understand. Therefore, unintelligible things are hard to understand. A coded message is unintelligible if you don't know the code. A whisper in a loud room is unintelligible. A weird sentence like "The waffles ran away from the Easter basket" is unintelligible because it doesn't make any sense. If you can't hear or understand something, it's unintelligible (and probably frustrating too).