Different MySQL index sizes after restore
Random insert into or delete from a secondary index can cause the index fragmentation. Basically it will use extra space than required. There are several ways to reclaim this space. One of the way to reclaim space is, taking mysqldump and restoring it. This helps to reclaim the space. 

As far as the restoration completed without any error this should be fine and you don't need to worry. 

For more information on fragmentation you can refer to below link.
https://dev.mysql.com/doc/refman/5.6/en/innodb-file-defragmenting.html
https://dev.mysql.com/doc/refman/5.6/en/myisam-optimization.html