mysql workbench migration changed my database. Can I trust it? I'm migrating a large production database(s) from mysql 5.5 to 5.6.
Used Mysql Workbench Migration Wizard which creates a shell script to run on source and taget machines.

The process worked well but there are major changes to the database:

For example:


Changed order of fields in primary key
PRIMARY KEY (ru_sid,ru_rule_id), =>   PRIMARY KEY (ru_rule_id,ru_sid)
Messed encoding while the data is expected to be utf8
I did a query of the same data in the original and new server and the output is different:
Pré-Home Flash Sales => PrÃ©-Home Flash Sales


Possibly there are other changes.

My question is - how can I tell if the migration is trustable. I cant check every table to see if changes in the index will not break something in my code. 
Can the workbench migration be trusted ?
Is there a better way to do the migration? What would you do?

EDIT:
Create statement before:
 (I removed the fields that are the same in the before and after)

CREATE TABLErules(
ru_rule_idint(10) unsigned NOT NULL AUTO_INCREMENT,
ru_titlevarchar(254) COLLATE utf8_unicode_ci NOT NULL DEFAULT '',
ru_datatext COLLATE utf8_unicode_ci NOT NULL,
ru_namevarchar(64) COLLATE utf8_unicode_ci NOT NULL,
ru_tagsvarchar(64) COLLATE utf8_unicode_ci DEFAULT '',
ru_priorityvarchar(12) COLLATE utf8_unicode_ci NOT NULL DEFAULT '1',
  PRIMARY KEY (ru_sid,ru_rule_id),
  KEYnum(ru_rule_id) USING BTREE
) ENGINE=MyISAM AUTO_INCREMENT=9998 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;


Create statement after:

CREATE TABLErules(
ru_rule_idint(10) unsigned NOT NULL AUTO_INCREMENT,
ru_titlevarchar(254) CHARACTER SET utf8 NOT NULL DEFAULT '',
ru_datatext CHARACTER SET utf8 NOT NULL,
ru_namevarchar(64) CHARACTER SET utf8 NOT NULL,
ru_tagsvarchar(64) CHARACTER SET utf8 DEFAULT '',
ru_priorityvarchar(12) CHARACTER SET utf8 NOT NULL DEFAULT '1',
  PRIMARY KEY (ru_rule_id,ru_sid),
  KEYnum(ru_rule_id)
) ENGINE=MyISAM AUTO_INCREMENT=9954 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
Seems you've found a bug in migration wizard, I follow your description and I was able to repeat issue on my machine. Can you please fill bug report at bugs.mysql.com? Appreciate. We'll do our best to fix that isse.
As workaround you can try this way - use Data Export to export only structure of your database. Run exported stricpt on target server. Then run migration wizard normally, but skip create target schema step. Let me know if that works for you.