Comment 1 for bug 1004910

This is not a bug as the backup of the ibd file is probably not clean (the test case doesn't ensure it).

Quoting from manual ( http://dev.mysql.com/doc/mysql-enterprise-backup/3.5/en/partial.restoring.single.html ):
If you have a *clean* backup of an .ibd file, you can restore it to the MySQL installation from which it originated as follows:

In this context, a clean.ibd file backup means:

There are no uncommitted modifications by transactions in the .ibd file.

There are no unmerged insert buffer entries in the .ibd file.

Purge has removed all delete-marked index records from the .ibd file.

mysqld has flushed all modified pages of the .ibd file from the buffer pool to the file.

You can make such a clean backup .ibd file with the following method:

Stop all activity from the mysqld server and commit all transactions.

Wait until SHOW INNODB STATUS shows that there are no active transactions in the database, and the main thread status of InnoDB is Waiting for server activity. Then you can make a copy of the .ibd file.

Another method for making a clean copy of an .ibd file is to use ibbackup:

Use ibbackup to back up the InnoDB installation.

Run ibbackup --apply-log to create a consistent version of the backup database.

Start a second (dummy) mysqld server on the backup and let it clean up the .ibd files in the backup. Wait for the cleanup to end.

Shut down the dummy mysqld server.

Take a clean .ibd file from the backup.