innodb_file_per_table option enabled but ibdata1 file still grows up
A number of operations use ibdata1 temporarily.  The actual data for the given table will be entirely in the .ibd file.

It's rather normal for ibdata1 to be at least tens of MB, even with all tables in their .ibd files.

Do you have the following case?


innodb_file_per_table=OFF
Create and populate table1 -- this will go into ibdata1
change to innodb_file_per_table=ON
Create and populate table2 -- this will go into table2.ibd
insert into table1 -- this will still go into ibdata1


The way to move an existing table to ibd is to set ON, then do

ALTER TABLE table1 ENGINE=InnoDB;


If this does not explain your situation, please keep an eye on (1) what operations are being performed on any table, and (2) the size of ibdata1.  If it grows again, the (1) may give us some more clues.

Note especially any operations involving large tables.