You know that long running query on your server, the one with a group by and a large join? It was probably creating a very large temp table on disk. How large was it? It is hard to tell. If the temp table has spilled to disk and you can login to the server, then you can check the size of the temp table file.
I prefer to monitor this and have mysqld enforce a limit. Who wants to run out of disk space because of a 100G temp table? But MySQL provides no limits for this. You can use a separate file system for temp tables to limit their size. If you have not done that then I think you are stuck. I want to add an option to MySQL so that the max size of an on-disk temp table can be enforced. Options already exist for the max size of an in-memory temp table.