As with my other databases it should be no surprise that when using MySQL InnoDB as your database engine, the system tablespace (ibdata files) never release space back to the operating system. The filesystem space will increase as needed, if defined by the autoextend property but will never reduce.
What is surprising, is there is no tool to shrink or release the free space back to the operating system. In Microsoft SQL Server, they have a shrink utility, in MongoDB you have the repairdatabase statement. With MySQL InnoDB your option is to dump and restore the database.