ibdata1 back to it's original size after deleting it
Did you have innodb_file_per_table = ON?

Regardless of the above setting, ibdata1 will have some stuff in it.  Without more specifics (size of that file, the above setting, number of tables, number of .ibd files, etc.), I cannot be more specific.

In my opinion, "tiny" tables may as well be built with file_per_table = OFF.