ibdata1 increases when firing update queries
Lets try to understand whats stored inside ibdata1:
When you have innodb_file_per_table enabled, the tables are stored in their own tablespace but the shared tablespace is still used to store other InnoDB’s internal data:
* data dictionary
* change buffer
* doublewrite buffer
* undo logs

since there is trancations, rollbacks that support repeatable read that will make ibdata1 files grow even when you update any innodb table.

reference: 
http://www.percona.com/blog/2013/08/20/why-is-the-ibdata1-file-continuously-growing-in-mysql/

ibdata1 grows exponentially when innodb_file_per_table is configured

https://serverfault.com/questions/272146/why-ibdata1-is-still-growing-when-i-have-used-innodb-file-per-table-in-mysql-5-1