When using an import file that contains a list of "distinguishedname" attributes that includes OUs, any users whose distinguishedname contains a comma is not shown as being in the correct OU when the file is imported. Instead, any users with commas in their DNs appear as being in the root. When the objects are migrated, everything will work as it should, but the GUI is misleading.
This is a known issue, and is only a visual/GUI problem. You can continue to migrate objects using distinguishedname import files.
Enhancement request ST38635 has been submitted to Development for consideration in a future release of Migration Manager for AD.