It may happen that your mysql instances face some diskspace problems. Usually this is an application-side problem. Following steps may help to identify the bogus points.
Show databases and their sizes
SELECT table_schema "DB Name", Round(Sum(data_length + index_length) / 1024 / 1024, 1) "DB Size in MB" FROM information_schema.tables GROUP BY table_schema;
Display table information
show table status;
Here you can see the raw table size (Data_length) in byte and corresponding index size (Index_length) f.e.
If you have binary log writing enabled, it may write a lot of data to disk (a separate one in best case). Especially if there is a lot of data getting changed, this can be much bigger than the database itself.