Meaning/Usage: A source of trouble or annoyance; used to indicate that something bothers you very much. "Ass" can be seen as profanity, so another way of saying this would be "Pain in the butt" or "Pain in the neck."
Explanation: When something gives you trouble and bothers you a lot, it gives you pain. To look for more colorful ways to express this, people started saying "pain in the neck." Another variation came out when people started to say "Pain in the rear end." This later became "Pain in the butt" or "Pain in the ass."