my understanding is that in MySQL an index field has to contain unique values. you should remove any duplicate keys before adding the index, or the following statement would create the index, ignore errors, deleting duplicate rows automatically!
ALTER IGNORE TABLE table_name ADD UNIQUE INDEX(field_name);
http://mysql.mirror.nedlinux****/doc/...ATE_INDEX.html
if this is not appropriate, then you are looking have an index field with duplicate values. I don't know that answer.