This is the major issue with the Innodb engine, the bulk delete/truncate operation will deleted the data but it is not reclaiming the space from the Innodb file. There are some techniques to reclaim the space but please make sure you must have the extra space on your servers.
1. Alter Database Set Engine = Innodb
2. Instead of truncate use the DROP statement.
3. Migrate your MySQL databases to another server MySQL server using MySQL dump utility and remove the ibdata file. Further migrate the backup database to orginal server which will makes the ibdata1 file fully de-fragmented.