Migration script bug: incorrect method called for index.
See this line:
https://code.vtiger.com/vtiger/vtigercrm/blob/master/modules/Migration/schema/660_to_700.php#L1783
You are calling the method Vtiger_Utils::TableHasForeignKey()
to check for the presence of an index...
Looking at the method I do not think this is ever going to return true.